Mercurial > repos > genouest > askor_de
changeset 0:ceef9bc6bbc7 draft
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/askor commit 08a187f91ba050d584e586d2fcc99d984dac607c
| author | genouest |
|---|---|
| date | Thu, 12 Apr 2018 05:23:45 -0400 |
| parents | |
| children | 6bbc90a11c3f |
| files | AskoR.R AskoR_DE.R askor_de.xml test-data/AskoAvsK.txt test-data/AskoT1AvsT1K.txt test-data/AskoT1vsT0.txt test-data/AskoT1vsT2.txt test-data/Contrasts.txt test-data/Samples.txt test-data/condition.asko.txt test-data/context.asko.txt test-data/contrast.asko.txt test-data/counts.csv test-data/out.pdf |
| diffstat | 14 files changed, 2010 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AskoR.R Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,651 @@ +asko3c <- function(data_list){ + asko<-list() + + ######### Condition ############ + + condition<-unique(data_list$samples$condition) # retrieval of different condition's names + col1<-which(colnames(data_list$samples)=="condition") # determination of number of the column "condition" + colcol<-which(colnames(data_list$samples)=="color") + if(is.null(parameters$fileofcount)){ + col2<-which(colnames(data_list$samples)=="file") # determination of number of the column "replicate" + column_name<-colnames(data_list$samples[,c(-col1,-col2,-colcol)]) # retrieval of column names needful to create the file condition + }else{column_name<-colnames(data_list$samples[,c(-col1,-colcol)])} + condition_asko<-data.frame(row.names=condition) # initialization of the condition's data frame + #level<-list() # initialization of the list will contain the level + # of each experimental factor + for (name in column_name){ # for each experimental factor : + # if(str_detect(name, "condition")){ # for the column of conditions, the level is fixed to 0 because + # level<-append(level, 0) # "condition" must be the first column of the data frame + # }else{ # + # level<-append(level, length(levels(data_list$samples[,name]))) # adding to the list the level of other experimental factors + # } + # + condition_asko$n<-NA # initialization of new column in the condition's data frame + colnames(condition_asko)[colnames(condition_asko)=="n"]<-name # to rename the new column with with the name of experimental factor + for(condition_name in condition){ # for each condition's names + condition_asko[condition_name,name]<-as.character(unique(data_list$samples[data_list$samples$condition==condition_name, name])) + } # filling the condition's data frame + } + # order_level<-order(unlist(level)) # list to vector + # condition_asko<-condition_asko[,order_level] # order columns according to their level + #asko$condition<-condition_asko # adding data frame of conditions to asko object + + #print(condition_asko) + + + #############contrast + context################## + i=0 + + contrast_asko<-data.frame(row.names = colnames(data_list$contrast)) # initialization of the contrast's data frame + contrast_asko$Contrast<-NA # all columns are created et initialized with + contrast_asko$context1<-NA # NA values + contrast_asko$context2<-NA # + + list_context<-list() # initialization of context and condition lists + list_condition<-list() # will be used to create the context data frame + if(parameters$mk_context==TRUE){ + for (contrast in colnames(data_list$contrast)){ # for each contrast : + i=i+1 # contrast data frame will be filled line by line + #print(contrast) + set_cond1<-row.names(data_list$contrast)[data_list$contrast[,contrast]>0] # retrieval of 1st set of condition's names implicated in a given contrast + set_cond2<-row.names(data_list$contrast)[data_list$contrast[,contrast]<0] # retrieval of 2nd set of condition's names implicated in a given contrast + parameters<-colnames(condition_asko) # retrieval of names of experimental factor + print(paste("set_cond1 : ", set_cond1, sep = "")) + # print(length(set_cond1)) + print(paste("set_cond2 : ", set_cond2, sep = "")) + # print(length(set_cond2)) + if(length(set_cond1)==1){complex1=F}else{complex1=T}# to determine if we have complex contrast (multiple conditions + if(length(set_cond2)==1){complex2=F}else{complex2=T}# compared to multiple conditions) or not + #print(complex1) + if(complex1==F && complex2==F){ # Case 1: one condition against one condition + contrast_asko[i,"context1"]<-set_cond1 # filling contrast data frame with the name of the 1st context + contrast_asko[i,"context2"]<-set_cond2 # filling contrast data frame with the name of the 2nd context + contrast_name<-paste(set_cond1,set_cond2, sep = "vs") # creation of contrast name by associating the names of contexts + contrast_asko[i,"Contrast"]<-contrast_name # filling contrast data frame with contrast name + list_context<-append(list_context, set_cond1) # + list_condition<-append(list_condition, set_cond1) # adding respectively to the lists "context" and "condition" the context name + list_context<-append(list_context, set_cond2) # and the condition name associated + list_condition<-append(list_condition, set_cond2) # + } + if(complex1==F && complex2==T){ # Case 2: one condition against multiple condition + contrast_asko[i,"context1"]<-set_cond1 # filling contrast data frame with the name of the 1st context + list_context<-append(list_context, set_cond1) # adding respectively to the lists "context" and "condition" the 1st context + list_condition<-append(list_condition, set_cond1) # name and the condition name associated + l=0 + # "common_factor" will contain the common experimental factors shared by + common_factor=list() # conditions belonging to the complex context + for (param_names in parameters){ # for each experimental factor + facteur<-unique(c(condition_asko[,param_names])) # retrieval of possible values for the experimental factor + l=l+1 # + for(value in facteur){ # for each possible values + verif<-unique(str_detect(set_cond2, value)) # verification of the presence of values in each condition contained in the set + if(length(verif)==1 && verif==TRUE){common_factor[l]<-value} # if verif contains only TRUE, value of experimental factor + } # is added as common factor + } + if(length(common_factor)>1){ # if there are several common factor + common_factor<-toString(common_factor) # the list is converted to string + contx<-str_replace(common_factor,", ","") + contx<-str_replace_all(contx, "NULL", "")}else{contx<-common_factor} # and all common factor are concatenated to become the name of context + contrast_asko[i,"context2"]<-contx # filling contrast data frame with the name of the 2nd context + contrast_name<-paste(set_cond1,contx, sep = "vs") # concatenation of context names to make the contrast name + contrast_asko[i,"Contrast"]<-contrast_name # filling contrast data frame with the contrast name + for(j in 1:length(set_cond2)){ # for each condition contained in the complex context (2nd): + list_context<-append(list_context, contx) # adding condition name with the context name associated + list_condition<-append(list_condition, set_cond2[j]) # to their respective list + } + } + if(complex1==T && complex2==F){ # Case 3: multiple conditions against one condition + contrast_asko[i,"context2"]<-set_cond2 # filling contrast data frame with the name of the 2nd context + list_context<-append(list_context, set_cond2) # adding respectively to the lists "context" and "condition" the 2nd context + list_condition<-append(list_condition, set_cond2) # name and the 2nd condition name associated + l=0 + # "common_factor" will contain the common experimental factors shared by + common_factor=list() # conditions belonging to the complex context + for (param_names in parameters){ # for each experimental factor: + facteur<-unique(c(condition_asko[,param_names])) # retrieval of possible values for the experimental factor + l=l+1 + for(value in facteur){ # for each possible values: + verif<-unique(str_detect(set_cond1, value)) # verification of the presence of values in each condition contained in the set + if(length(verif)==1 && verif==TRUE){common_factor[l]<-value} # if verif contains only TRUE, value of experimental factor + } # is added as common factor + } + if(length(common_factor)>1){ # if there are several common factor + common_factor<-toString(common_factor) # the list is converted to string + contx<-str_replace(common_factor,", ","") + contx<-str_replace_all(contx, "NULL", "")}else{contx<-common_factor} # and all common factor are concatenated to become the name of context + contrast_asko[i,"context1"]<-contx # filling contrast data frame with the name of the 1st context + contrast_name<-paste(contx,set_cond2, sep = "vs") # concatenation of context names to make the contrast name + contrast_asko[i,"Contrast"]<-contrast_name # filling contrast data frame with the contrast name + for(j in 1:length(set_cond1)){ # for each condition contained in the complex context (1st): + list_context<-append(list_context, contx) # adding condition name with the context name associated + list_condition<-append(list_condition, set_cond1[j]) # to their respective list + } + } + if(complex1==T && complex2==T){ # Case 4: multiple conditions against multiple conditions + m=0 # + n=0 # + common_factor1=list() # list of common experimental factors shared by conditions of the 1st context + common_factor2=list() # list of common experimental factors shared by conditions of the 2nd context + w=1 + for (param_names in parameters){ # for each experimental factor: + print(w) + w=w+1 + facteur<-unique(c(condition_asko[,param_names])) # retrieval of possible values for the experimental factor + print(paste("facteur : ", facteur, sep="")) + for(value in facteur){ # for each possible values: + print(value) + #print(class(value)) + #print(set_cond1) + verif1<-unique(str_detect(set_cond1, value)) # verification of the presence of values in each condition + # contained in the 1st context + verif2<-unique(str_detect(set_cond2, value)) # verification of the presence of values in each condition + # contained in the 2nd context + + if(length(verif1)==1 && verif1==TRUE){m=m+1;common_factor1[m]<-value} # if verif=only TRUE, value of experimental factor is added as common factor + if(length(verif2)==1 && verif2==TRUE){n=n+1;common_factor2[n]<-value} # if verif=only TRUE, value of experimental factor is added as common factor + } + } + print(paste("common_factor1 : ",common_factor1,sep="")) + print(paste("common_factor2 : ",common_factor2,sep="")) + + if(length(common_factor1)>1){ # if there are several common factor for conditions in the 1st context + common_factor1<-toString(common_factor1) # conversion list to string + contx1<-str_replace(common_factor1,", ","")}else{contx1<-common_factor1}# all common factor are concatenated to become the name of context + contx1<-str_replace_all(contx1, "NULL", "") + print(paste("contx1 : ", contx1, sep="")) + if(length(common_factor2)>1){ # if there are several common factor for conditions in the 2nd context + common_factor2<-toString(common_factor2) # conversion list to string + contx2<-str_replace(common_factor2,", ","")}else{contx2<-common_factor2}# all common factor are concatenated to become the name of context + contx2<-str_replace_all(contx2, "NULL", "") + print(paste("contx2 : ", contx2, sep="")) + contrast_asko[i,"context1"]<-contx1 # filling contrast data frame with the name of the 1st context + contrast_asko[i,"context2"]<-contx2 # filling contrast data frame with the name of the 2nd context + contrast_asko[i,"Contrast"]<-paste(contx1,contx2, sep = "vs") # filling contrast data frame with the name of the contrast + for(j in 1:length(set_cond1)){ # for each condition contained in the complex context (1st): + list_context<-append(list_context, contx1) # verification of the presence of values in each condition + list_condition<-append(list_condition, set_cond1[j]) # contained in the 1st context + } + for(j in 1:length(set_cond2)){ # for each condition contained in the complex context (2nd): + list_context<-append(list_context, contx2) # verification of the presence of values in each condition + list_condition<-append(list_condition, set_cond2[j]) # contained in the 1st context + } + } + } + } + else{ + for (contrast in colnames(data_list$contrast)){ + i=i+1 + contexts=strsplit2(contrast,"vs") + contrast_asko[i,"Contrast"]<-contrast + contrast_asko[i,"context1"]=contexts[1] + contrast_asko[i,"context2"]=contexts[2] + set_cond1<-row.names(data_list$contrast)[data_list$contrast[,contrast]>0] + set_cond2<-row.names(data_list$contrast)[data_list$contrast[,contrast]<0] + for (cond1 in set_cond1){ +# print(contexts[1]) + # print(cond1) + list_context<-append(list_context, contexts[1]) + list_condition<-append(list_condition, cond1) + } + for (cond2 in set_cond2){ + list_context<-append(list_context, contexts[2]) + list_condition<-append(list_condition, cond2) + } + } + } + + list_context<-unlist(list_context) # conversion list to vector + list_condition<-unlist(list_condition) # conversion list to vector +# print(list_condition) +# print(list_context) + context_asko<-data.frame(list_context,list_condition) # creation of the context data frame + context_asko<-unique(context_asko) + colnames(context_asko)[colnames(context_asko)=="list_context"]<-"context" # header formatting for askomics + colnames(context_asko)[colnames(context_asko)=="list_condition"]<-"condition" # header formatting for askomics + #asko$contrast<-contrast_asko # adding context data frame to asko object + #asko$context<-context_asko # adding context data frame to asko object + asko<-list("condition"=condition_asko, "contrast"=contrast_asko, "context"=context_asko) + colnames(context_asko)[colnames(context_asko)=="context"]<-"Context" # header formatting for askomics + colnames(context_asko)[colnames(context_asko)=="condition"]<-"has@Condition" # header formatting for askomics + colnames(contrast_asko)[colnames(contrast_asko)=="context1"]<-paste("context1_of", "Context", sep="@") # header formatting for askomics + colnames(contrast_asko)[colnames(contrast_asko)=="context2"]<-paste("context2_of", "Context", sep="@") # header formatting for askomics + + ######## Files creation ######## + + write.table(data.frame("Condition"=row.names(condition_asko),condition_asko), paste0(parameters$out_dir,"/condition.asko.txt"), sep = parameters$sep, row.names = F, quote=F) # creation of condition file for asko + write.table(context_asko, paste0(parameters$out_dir,"/context.asko.txt"), sep=parameters$sep, col.names = T, row.names = F,quote=F) # creation of context file for asko + write.table(contrast_asko, paste0(parameters$out_dir,"/contrast.asko.txt"), sep=parameters$sep, col.names = T, row.names = F, quote=F) # creation of contrast file for asko + return(asko) +} + +.NormCountsMean <- function(glmfit, ASKOlist, context){ + + lib_size_norm<-glmfit$samples$lib.size*glmfit$samples$norm.factors # normalization computation of all library sizes + set_condi<-ASKOlist$context$condition[ASKOlist$context$context==context] # retrieval of condition names associated to context + + for (condition in set_condi){ + sample_name<-rownames(glmfit$samples[glmfit$samples$condition==condition,]) # retrieval of the replicate names associated to conditions + subset_counts<-data.frame(row.names = row.names(glmfit$counts)) # initialization of data frame as subset of counts table + for(name in sample_name){ + lib_sample_norm<-glmfit$samples[name,"lib.size"]*glmfit$samples[name,"norm.factors"] # normalization computation of sample library size + subset_counts$c<-glmfit$counts[,name] # addition in subset of sample counts column + subset_counts$c<-subset_counts$c*mean(lib_size_norm)/lib_sample_norm # normalization computation of sample counts + colnames(subset_counts)[colnames(subset_counts)=="c"]<-name # to rename the column with the condition name + } + mean_counts<-rowSums(subset_counts)/ncol(subset_counts) # computation of the mean + ASKOlist$stat.table$mean<-mean_counts # subset integration in the glm_result table + colnames(ASKOlist$stat.table)[colnames(ASKOlist$stat.table)=="mean"]<-paste(context,condition,sep = "/") + } # to rename the column with the context name + return(ASKOlist$stat.table) # return the glm object +} + +AskoStats <- function (glm_test, fit, contrast, ASKOlist, dge,parameters){ + contrasko<-ASKOlist$contrast$Contrast[row.names(ASKOlist$contrast)==contrast] # to retrieve the name of contrast from Asko object + contx1<-ASKOlist$contrast$context1[row.names(ASKOlist$contrast)==contrast] # to retrieve the name of 1st context from Asko object + contx2<-ASKOlist$contrast$context2[row.names(ASKOlist$contrast)==contrast] # to retrieve the name of 2nd context from Asko object + + ASKO_stat<-glm_test$table + ASKO_stat$Test_id<-paste(contrasko, rownames(ASKO_stat), sep = "_") # addition of Test_id column = unique ID + ASKO_stat$contrast<-contrasko # addition of the contrast of the test + ASKO_stat$gene <- row.names(ASKO_stat) # addition of gene column = gene ID + ASKO_stat$FDR<-p.adjust(ASKO_stat$PValue, method=parameters$p_adj_method) # computation of False Discovery Rate + + ASKO_stat$Significance=0 # Between context1 and context2 : + ASKO_stat$Significance[ASKO_stat$logFC< 0 & ASKO_stat$FDR<=parameters$threshold_FDR] = -1 # Significance values = -1 for down regulated genes + ASKO_stat$Significance[ASKO_stat$logFC> 0 & ASKO_stat$FDR<=parameters$threshold_FDR] = 1 # Significance values = 1 for up regulated genes + + if(parameters$Expression==TRUE){ + ASKO_stat$Expression=NA # addition of column "expression" + ASKO_stat$Expression[ASKO_stat$Significance==-1]<-paste(contx1, contx2, sep="<") # the value of attribute "Expression" is a string + ASKO_stat$Expression[ASKO_stat$Significance==1]<-paste(contx1, contx2, sep=">") # this attribute is easier to read the Significance + ASKO_stat$Expression[ASKO_stat$Significance==0]<-paste(contx1, contx2, sep="=") # of expression between two contexts + } + if(parameters$logFC==T){cola="logFC"}else{cola=NULL} # + if(parameters$FC==T){colb="FC";ASKO_stat$FC <- 2^abs(ASKO_stat$logFC)}else{colb=NULL} # computation of Fold Change from log2FC + if(parameters$Sign==T){colc="Significance"} # + if(parameters$logCPM==T){cold="logCPM"}else{cold=NULL} # + if(parameters$LR==T){cole="LR"}else{cole=NULL} # + if(parameters$FDR==T){colf="FDR"}else{colf=NULL} + + ASKOlist$stat.table<-ASKO_stat[,c("Test_id","contrast","gene",cola,colb,"PValue", # adding table "stat.table" to the ASKOlist + "Expression",colc,cold,cole,colf)] + if(parameters$mean_counts==T){ # computation of the mean of normalized counts for conditions + ASKOlist$stat.table<-.NormCountsMean(fit, ASKOlist, contx1) # in the 1st context + ASKOlist$stat.table<-.NormCountsMean(fit, ASKOlist, contx2) # in the 2nd context + } + print(table(ASKO_stat$Expression)) + colnames(ASKOlist$stat.table)[colnames(ASKOlist$stat.table)=="gene"] <- paste("is", "gene", sep="@") # header formatting for askomics + colnames(ASKOlist$stat.table)[colnames(ASKOlist$stat.table)=="contrast"] <- paste("measured_in", "Contrast", sep="@") # header formatting for askomics + o <- order(ASKOlist$stat.table$FDR) # ordering genes by FDR value + ASKOlist$stat.table<-ASKOlist$stat.table[o,] + # + dir.create(parameters$out_dir) + write.table(ASKOlist$stat.table,paste0(parameters$out_dir,"/", parameters$organism, contrasko, ".txt"), # + sep=parameters$sep, col.names = T, row.names = F, quote=FALSE) + + if(parameters$heatmap==TRUE){ + cpm_gstats<-cpm(dge, log=TRUE)[o,][1:parameters$numhigh,] + heatmap.2(cpm_gstats, cexRow=0.5, cexCol=0.8, scale="row", labCol=dge$samples$Name, xlab=contrast, Rowv = FALSE, dendrogram="col") + } + + return(ASKOlist) + +} + +loadData <- function(parameters){ + + #####samples##### + samples<-read.table(parameters$sample_file, header=TRUE, sep="\t", row.names=1, comment.char = "#") #prise en compte des r?sultats de T2 + if(is.null(parameters$select_sample)==FALSE){ + if(parameters$regex==TRUE){ + selected<-c() + for(sel in parameters$select_sample){ + select<-grep(sel, rownames(samples)) + if(is.null(selected)){selected=select}else{selected<-append(selected, select)} + } + samples<-samples[selected,] + }else{samples<-samples[parameters$select_sample,]} + } + + if(is.null(parameters$rm_sample)==FALSE){ + if(parameters$regex==TRUE){ + for(rm in parameters$rm_sample){ + removed<-grep(rm, rownames(samples)) +# print(removed) + if(length(removed!=0)){samples<-samples[-removed,]} + } + }else{ + for (rm in parameters$rm_sample) { + rm2<-match(rm, rownames(samples)) + samples<-samples[-rm2,] + } + } + } + condition<-unique(samples$condition) + #print(condition) + color<-brewer.pal(length(condition), parameters$palette) + #print(color) + samples$color<-NA + j=0 + for(name in condition){ + j=j+1 + samples$color[samples$condition==name]<-color[j] + } + #print(samples) + + + #####counts##### + if(is.null(parameters$fileofcount)){ + dge<-readDGE(samples$file, labels=rownames(samples), columns=c(parameters$col_genes,parameters$col_counts), header=TRUE, comment.char="#") + dge<-DGEList(counts=dge$counts, samples=samples) + # dge$samples=samples + #countT<-dge$counts + # if(is.null(parameters$select_sample)==FALSE){ + # slct<-grep(parameters$select_sample, colnames(countT)) + # dge$counts<-dge$counts[,slct] + # dge$samples<-dge$samples[,slct] + # } + # if(is.null(parameters$rm_sample)==FALSE){ + # rmc<-grep(parameters$rm_count, colnames(dge$counts)) + # dge$counts<-dge$counts[,-rmc] + # print(ncol(dge$counts)) + # rms<-grep(parameters$rm_sample, row.names(dge$samples)) + # dge$samples<-dge$samples[-rms,] + # } + }else { + if(grepl(".csv", parameters$fileofcount)==TRUE){ + count<-read.csv(parameters$fileofcount, header=TRUE, sep = "\t", row.names = parameters$col_genes) + } + else{ + count<-read.table(parameters$fileofcount, header=TRUE, sep = "\t", row.names = parameters$col_genes, comment.char = "") + } + select_counts<-row.names(samples) + #countT<-count[,c(parameters$col_counts:length(colnames(count)))] + countT<-count[,select_counts] + dge<-DGEList(counts=countT, samples=samples) + # if(is.null(parameters$select_sample)==FALSE){ + # slct<-grep(parameters$select_sample, colnames(countT)) + # countT<-countT[,slct] + # } + # if(is.null(parameters$rm_count)==FALSE){ + # rms<-grep(parameters$rm_count, colnames(countT)) + # #print(rms) + # countT<-countT[,-rms] + # + # } + #print(nrow(samples)) + #print(ncol(countT)) + } + + #####design##### + Group<-factor(samples$condition) + designExp<-model.matrix(~0+Group) + rownames(designExp) <- row.names(samples) + colnames(designExp) <- levels(Group) + + #####contrast##### + contrastab<-read.table(parameters$contrast_file, sep="\t", header=TRUE, row.names = 1, comment.char="#", stringsAsFactors = FALSE) + + rmcol<-list() + for(condition_name in row.names(contrastab)){ + test<-match(condition_name, colnames(designExp),nomatch = 0) + if(test==0){ + print(condition_name) + rm<-grep("0", contrastab[condition_name,], invert = T) + print(rm) + if(is.null(rmcol)){rmcol=rm}else{rmcol<-append(rmcol, rm)} + } + } + if (length(rmcol)> 0){ + rmcol<-unlist(rmcol) + rmcol<-unique(rmcol) + rmcol=-rmcol + contrastab<-contrastab[,rmcol] + } + + ord<-match(colnames(designExp),row.names(contrastab), nomatch = 0) + contrast_table<-contrastab[ord,] + colnum<-c() + + for(contrast in colnames(contrast_table)){ + set_cond1<-row.names(contrast_table)[contrast_table[,contrast]=="+"] + #print(set_cond1) + set_cond2<-row.names(contrast_table)[contrast_table[,contrast]=="-"] + #print(set_cond2) + if(length(set_cond1)!=length(set_cond2)){ + contrast_table[,contrast][contrast_table[,contrast]=="+"]=signif(1/length(set_cond1),digits = 2) + contrast_table[,contrast][contrast_table[,contrast]=="-"]=signif(-1/length(set_cond2),digits = 2) + } + else { + contrast_table[,contrast][contrast_table[,contrast]=="+"]=1 + contrast_table[,contrast][contrast_table[,contrast]=="-"]=-1 + } + contrast_table[,contrast]<-as.numeric(contrast_table[,contrast]) + } + + #####annotation##### + #annotation <- read.csv(parameters$annotation_file, header = T, sep = '\t', quote = "", row.names = 1) + + #data<-list("counts"=countT, "samples"=samples, "contrast"=contrast_table, "annot"=annotation, "design"=designExp) + #print(countT) + rownames(dge$samples)<-rownames(samples) #Â replace the renaming by files + data<-list("dge"=dge, "samples"=samples, "contrast"=contrast_table, "design"=designExp) + return(data) +} + +GEfilt <- function(dge_list, parameters){ + cpm<-cpm(dge_list) + logcpm<-cpm(dge_list, log=TRUE) + colnames(logcpm)<-rownames(dge_list$samples) + nsamples <- ncol(dge_list) # cr?ation nouveau plot + plot(density(logcpm[,1]), + col=as.character(dge_list$samples$color[1]), # plot exprimant la densit? de chaque g?ne + lwd=1, + ylim=c(0,0.21), + las=2, + main="A. Raw data", + xlab="Log-cpm") # en fonction de leurs valeurs d'expression + abline(v=0, lty=3) + for (i in 2:nsamples){ # on boucle sur chaque condition restante + den<-density(logcpm[,i]) # et les courbes sont rajout?es dans le plot + lines(den$x, col=as.character(dge_list$samples$color[i]), den$y, lwd=1) # + } + legend("topright", rownames(dge_list$samples), + text.col=as.character(dge_list$samples$color), + bty="n", + text.width=6, + cex=0.5) + # rowSums compte le nombre de score (cases) pour chaque colonne Sup ? 0.5 + keep.exprs <- rowSums(cpm>parameters$threshold_cpm)>=parameters$replicate_cpm # en ajoutant >=3 cela donne un test conditionnel + filtered_counts <- dge_list[keep.exprs,,keep.lib.sizes=F] # si le comptage respecte la condition alors renvoie TRUE + filtered_cpm<-cpm(filtered_counts$counts, log=TRUE) + + plot(density(filtered_cpm[,1]), + col=as.character(dge_list$samples$color[1]), + lwd=2, + ylim=c(0,0.21), + las=2, + main="B. Filtered data", xlab="Log-cpm") + abline(v=0, lty=3) + for (i in 2:nsamples){ + den <- density(filtered_cpm[,i]) + lines(den$x,col=as.character(dge_list$samples$color[i]), den$y, lwd=1) + } + legend("topright", rownames(dge_list$samples), + text.col=as.character(dge_list$samples$col), + bty="n", + text.width=6, + cex=0.5) + return(filtered_counts) +} + +GEnorm <- function(filtered_GE, parameters){ + filtered_cpm <- cpm(filtered_GE, log=TRUE) #nouveau calcul Cpm sur donn?es filtr?es, si log=true alors valeurs cpm en log2 + colnames(filtered_cpm)<-rownames(filtered_GE$samples) + boxplot(filtered_cpm, + col=filtered_GE$samples$color, #boxplot des scores cpm non normalis?s + main="A. Before normalization", + cex.axis=0.5, + las=2, + ylab="Log-cpm") + + norm_GE<-calcNormFactors(filtered_GE, method = parameters$normal_method) # normalisation de nos comptages par le methode TMM, estimation du taux de production d'un ARN # en estimant l'?chelle des facteurs entre echantillons -> but : pouvoir comparer nos ech entre eux + + logcpm_norm <- cpm(norm_GE, log=TRUE) + colnames(logcpm_norm)<-rownames(filtered_GE$samples) + boxplot(logcpm_norm, + col=filtered_GE$samples$color, + main="B. After normalization", + cex.axis=0.5, + las=2, + ylab="Log-cpm") + + return(norm_GE) +} + +GEcorr <- function(dge, parameters){ + lcpm<-cpm(dge, log=TRUE) + colnames(lcpm)<-rownames(dge$samples) + cormat<-cor(lcpm) + # color<- colorRampPalette(c("yellow", "white", "green"))(20) + color<-colorRampPalette(c("black","red","yellow","white"),space="rgb")(28) + heatmap(cormat, col=color, symm=TRUE,RowSideColors =as.character(dge$samples$color), ColSideColors = as.character(dge$samples$color)) + #MDS + mds <- cmdscale(dist(t(lcpm)),k=3, eig=TRUE) + eigs<-round((mds$eig)*100/sum(mds$eig[mds$eig>0]),2) + + mds1<-ggplot(as.data.frame(mds$points), aes(V1, V2, label = rownames(mds$points))) + labs(title="MDS Axes 1 and 2") + geom_point(color =as.character(dge$samples$color) ) + xlab(paste('dim 1 [', eigs[1], '%]')) +ylab(paste('dim 2 [', eigs[2], "%]")) + geom_label_repel(aes(label = rownames(mds$points)), color = 'black',size = 3.5) + print(mds1) + #ggsave("mds_corr1-2.tiff") + #ggtitle("MDS Axes 2 and 3") + mds2<-ggplot(as.data.frame(mds$points), aes(V2, V3, label = rownames(mds$points))) + labs(title="MDS Axes 2 and 3") + geom_point(color =as.character(dge$samples$color) ) + xlab(paste('dim 2 [', eigs[2], '%]')) +ylab(paste('dim 3 [', eigs[3], "%]")) + geom_label_repel(aes(label = rownames(mds$points)), color = 'black',size = 3.5) + print(mds2) + # ggtitle("MDS Axes 1 and 3") + #ggsave("mds_corr2-3.tiff") + mds3<-ggplot(as.data.frame(mds$points), aes(V1, V3, label = rownames(mds$points))) + labs(title="MDS Axes 1 and 3") + geom_point(color =as.character(dge$samples$color) ) + xlab(paste('dim 1 [', eigs[1], '%]')) +ylab(paste('dim 3 [', eigs[3], "%]")) + geom_label_repel(aes(label = rownames(mds$points)), color = 'black',size = 3.5) + print(mds3) + #ggsave("mds_corr1-3.tiff") +} + +DEanalysis <- function(norm_GE, data_list, asko_list, parameters){ + + normGEdisp <- estimateDisp(norm_GE, data_list$design) + if(parameters$glm=="lrt"){ + fit <- glmFit(normGEdisp, data_list$design, robust = T) + } + if(parameters$glm=="qlf"){ + fit <- glmQLFit(normGEdisp, data_list$design, robust = T) + plotQLDisp(fit) + } + + #plotMD.DGEGLM(fit) + #plotBCV(norm_GE) + + #sum<-norm_GE$genes + for (contrast in colnames(data_list$contrast)){ + print(asko_list$contrast$Contrast[contrast]) + if(parameters$glm=="lrt"){ + glm_test<-glmLRT(fit, contrast=data_list$contrast[,contrast]) + } + if(parameters$glm=="qlf"){ + glm_test<-glmQLFTest(fit, contrast=data_list$contrast[,contrast]) + } + + #sum[,contrast]<-decideTestsDGE(glm, adjust.method = parameters$p_adj_method, lfc=1) + #print(table(sum[,contrast])) + AskoStats(glm_test, fit, contrast, asko_list,normGEdisp,parameters) + } +} + +Asko_start <-function(){ + library(limma) + library(statmod) + library(edgeR) + library(ggplot2) + library(RColorBrewer) + library(ggrepel) + library(gplots) + library(stringr) + library(optparse) + option_list = list( + make_option(c("-o", "--out"), type="character", default="out.pdf",dest="output_pdf", + help="output file name [default= %default]", metavar="character"), + make_option(c("-d", "--dir"), type="character", default=".",dest="dir_path", + help="data directory path [default= %default]", metavar="character"), + make_option("--outdir", type="character", default=".",dest="out_dir", + help="outputs directory [default= %default]", metavar="character"), + make_option(c("-O", "--org"), type="character", default="Asko", dest="organism", + help="Organism name [default= %default]", metavar="character"), + make_option(c("-f", "--fileofcount"), type="character", default=NULL, dest="fileofcount", + help="file of counts [default= %default]", metavar="character"), + make_option(c("-G", "--col_genes"), type="integer", default=1, dest="col_genes", + help="col of ids in count files [default= %default]", metavar="integer"), + make_option(c("-C", "--col_counts"), type="integer", default=7,dest="col_counts", + help="col of counts in count files [default= %default (featureCounts) ]", metavar="integer"), + make_option(c("-t", "--sep"), type="character", default="\t", dest="sep", + help="col separator [default= %default]", metavar="character"), + make_option(c("-a", "--annotation"), type="character", default="annotation.txt", dest="annotation_file", + help="annotation file [default= %default]", metavar="character"), + make_option(c("-s", "--sample"), type="character", default="Samples.txt", dest="sample_file", + help="Samples file [default= %default]", metavar="character"), + make_option(c("-c", "--contrasts"), type="character", default="Contrasts.txt",dest="contrast_file", + help="Contrasts file [default= %default]", metavar="character"), + make_option(c("-k", "--mk_context"), type="logical", default=FALSE,dest="mk_context", + help="generate automatically the context names [default= %default]", metavar="logical"), + make_option(c("-p", "--palette"), type="character", default="Set2", dest="palette", + help="Color palette (ggplot)[default= %default]", metavar="character"), + make_option(c("-R", "--regex"), type="logical", default=FALSE, dest="regex", + help="use regex when selecting/removing samples [default= %default]", metavar="logical"), + make_option(c("-S", "--select"), type="character", default=NULL, dest="select_sample", + help="selected samples [default= %default]", metavar="character"), + make_option(c("-r", "--remove"), type="character", default=NULL, dest="rm_sample", + help="removed samples [default= %default]", metavar="character"), + make_option(c("--th_cpm"), type="double", default=0.5, dest="threshold_cpm", + help="CPM's threshold [default= %default]", metavar="double"), + make_option(c("--rep"), type="integer", default=3, dest="replicate_cpm", + help="Minimum number of replicates [default= %default]", metavar="integer"), + make_option(c("--th_FDR"), type="double", default=0.05, dest="threshold_FDR", + help="FDR threshold [default= %default]", metavar="double"), + make_option(c("-n", "--normalization"), type="character", default="TMM", dest="normal_method", + help="normalization method (TMM/RLE/upperquartile/none) [default= %default]", metavar="character"), + make_option(c("--adj"), type="character", default="fdr", dest="p_adj_method", + help="p-value adjust method (holm/hochberg/hommel/bonferroni/BH/BY/fdr/none) [default= %default]", metavar="character"), + make_option("--glm", type="character", default="qlf", dest="glm", + help=" GLM method (lrt/qlf) [default= %default]", metavar="character"), + make_option(c("--lfc"), type="logical", default="TRUE", dest="logFC", + help="logFC in the summary table [default= %default]", metavar="logical"), + make_option("--fc", type="logical", default="TRUE", dest="FC", + help="FC in the summary table [default= %default]", metavar="logical"), + make_option(c("--lcpm"), type="logical", default="FALSE", dest="logCPM", + help="logCPm in the summary table [default= %default]", metavar="logical"), + make_option("--fdr", type="logical", default="TRUE", dest="FDR", + help="FDR in the summary table [default= %default]", metavar="logical"), + make_option("--lr", type="logical", default="FALSE", dest="LR", + help="LR in the summary table [default= %default]", metavar="logical"), + make_option(c("--sign"), type="logical", default="TRUE", dest="Sign", + help="Significance (1/0/-1) in the summary table [default= %default]", metavar="logical"), + make_option(c("--expr"), type="logical", default="TRUE", dest="Expression", + help="Significance expression in the summary table [default= %default]", metavar="logical"), + make_option(c("--mc"), type="logical", default="TRUE", dest="mean_counts", + help="Mean counts in the summary table [default= %default]", metavar="logical"), + make_option(c("--hm"), type="logical", default="TRUE", dest="heatmap", + help="generation of the expression heatmap [default= %default]", metavar="logical"), + make_option(c("--nh"), type="integer", default="50", dest="numhigh", + help="number of genes in the heatmap [default= %default]", metavar="integer") + ) + opt_parser = OptionParser(option_list=option_list) + parameters = parse_args(opt_parser) + + if(is.null(parameters$rm_sample) == FALSE ) { + str_replace_all(parameters$rm_sample, " ", "") + parameters$rm_sample<-strsplit2(parameters$rm_sample, ",") + } + + if(is.null(parameters$select_sample) == FALSE ) { + str_replace_all(parameters$select_sample, " ", "") + parameters$select_sample<-strsplit2(parameters$select_sample, ",") + } + + dir.create(parameters$out_dir) + return(parameters) +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AskoR_DE.R Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,44 @@ +askor_path<-Sys.getenv("ASKOR_PATH") +source(paste0(askor_path,"/AskoR.R")) + +############################################## +## Parameters ## +############################################## + +parameters<-Asko_start() +setwd(parameters$dir_path) +# source("/home/flegeai/local/askoR/askoStart.R") +#parameters$col_genes=1 +#parameters$col_counts=7 +# parameters$regex=FALSE +#parameters$rm_sample=list("T0_4", "T1K_4", "T1A_4", "T2A_4", "T2K_4", "T3K_4", "T3A_4") +# #parameters$select_sample=c("T0_4", "T1K_4", "T1A_4", "T2A_4", "T2K_4", "T3K_4", "T3A_4") +# #parameters$rm_sample=list("_4") +# parameters$organism = "Ap" +# parameters$fileofcount = NULL +# parameters$annotation_file = "annotation.txt" +# parameters$sample_file = "Samples.txt" +# parameters$contrast_file = "Contrasts.txt" +# parameters$mk_context="manual" +# parameters$glm="qlf" + + +######################################## +## Loading the data from the samples ##+ +######################################## + +data<-loadData(parameters) +cat("Total number of genes : ", dim(data$dge$counts)[1], "\n") +cat("Total number of samples : ", dim(data$dge$counts)[2], "\n") +cat("summary of CPM by samples\n") +summary(cpm(data$dge)) +pdf(parameters$output_pdf) +asko_data<-asko3c(data) +cat("Filtering genes with more than ", parameters$threshold_cpm, " CPM in ",parameters$replicate_cpm,"samples\n") +asko_filt<-GEfilt(data$dge, parameters) +cat("Total number of filtered genes : ", dim(asko_filt$counts)[1], "\n") +asko_norm<-GEnorm(asko_filt,parameters) +GEcorr(asko_norm,parameters) +cat("Statistical analysis\n") +DEanalysis(asko_norm,data, asko_data,parameters) +dev.off()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/askor_de.xml Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,165 @@ +<tool id="askor_de" name="AskoR DE" version="0.1"> + <description>EdgeR for AskOmics</description> + <requirements> + <requirement type="package" version="3.34.6">bioconductor-limma</requirement> + <requirement type="package" version="1.4.30">r-statmod</requirement> + <requirement type="package" version="3.20.7">bioconductor-edger</requirement> + <requirement type="package" version="2.2.1">r-ggplot2</requirement> + <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> + <requirement type="package" version="0.7.0">r-ggrepel</requirement> + <requirement type="package" version="3.0.1">r-gplots</requirement> + <requirement type="package" version="1.4.4">r-optparse</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + export ASKOR_PATH='$__tool_directory__' + + && + + Rscript '$__tool_directory__/AskoR_DE.R' + --out '${out_pdf}' + --outdir askor_output + --fileofcount '${fileofcounts}' + --sample '${samples}' + --contrasts '${contrasts}' + #if $adv.organism + --org '${adv.organism}' + #end if + #if $adv.colgenes + --col_genes ${adv.colgenes} + #end if + #if $adv.palette + --palette '${adv.palette}' + #end if + #if $selection.sel + --select '${selection.sel}' + #end if + #if $selection.remove + --remove '${selection.remove}' + #end if + #if $thresholds.th_cpm + --th_cpm ${thresholds.th_cpm} + #end if + #if $thresholds.rep + --rep ${thresholds.rep} + #end if + #if $thresholds.th_FDR + --th_FDR ${thresholds.th_FDR} + #end if + #if $stats.norm + --normalization '${stats.norm}' + #end if + #if $stats.adj + --adj '${stats.adj}' + #end if + #if $stats.glm + --glm '${stats.glm}' + #end if + #if $adv.nh + --nh ${adv.nh} + #end if + ]]></command> + <inputs> + <param format="csv" name="fileofcounts" type="data" label="File of counts" /> + <param format="tsv" name="samples" type="data" label="Descriptions of the samples" /> + <param format="tsv" name="contrasts" type="data" label="Descriptions of the contrasts" /> + <section name="adv" title="Format options" expanded="false"> + <param name="colgenes" type="integer" label="Column of the genes" value="1" optional="true" /> + <!--param name="sep" type="text" label="Field separator" value="\t" optional="true" /--> + <param name="palette" type="text" label="Color palette (Rcolorbrewer)" value="Set2" optional="true" /> + <param name="organism" type="text" label="Organism" value="Asko" optional="true" /> + <param name="nh" type="integer" label="Number of genes in the heatmap" value="50" optional="true" /> + </section> + <section name="selection" title="Samples selection options" expanded="false"> + <param name="sel" type="text" label="List of selected samples (separated by comma)" optional="true" /> + <param name="remove" type="text" label="List of removed samples (separated by comma)" optional="true" /> + </section> + <section name="thresholds" title="Threshold options" expanded="false"> + <param name="th_cpm" type="float" label="Minimum CPM value for selecting a gene" value="0.5" optional="true" /> + <param name="rep" type="integer" label="Number of samples with CPM > th_comp for selecting a gene" value="3" optional="true" /> + <param name="th_FDR" type="float" label="FDR threshold for reporting a differential gene" value="0.05" optional="true" /> + </section> + <section name="stats" title="Statistics options" expanded="false"> + <param name="norm" type="select" label="Normalization method"> + <option value="TMM">TMM</option> + <option value="RLE">RLE</option> + <option value="upperquartile">Upperquartile</option> + <option value="none">None</option> + </param> + <param name="glm" type="select" label="GLM method"> + <option value="qlf">qlf</option> + <option value="lrt">lrt</option> + </param> + <param name="adj" type="select" label="Multitest correction method"> + <option value="fdr">fdr</option> + <option value="holm">holm</option> + <option value="hochberg">hochberg</option> + <option value="hommel">hommel</option> + <option value="bonferroni">bonferroni</option> + <option value="BH">BH</option> + <option value="BY">BY</option> + <option value="none">none</option> + </param> + </section> + </inputs> + <outputs> + <data format="pdf" name="out_pdf" label="${tool.name} on ${on_string}: Graphics" /> + <data name="output" format="tsv" label="${tool.name} on ${on_string}"> + <discover_datasets pattern="(?P<designation>.+)\.txt" ext="tsv" visible="true" directory="askor_output" /> + </data> + </outputs> + <tests> + <test> + <param name="fileofcounts" ftype="csv" value="counts.csv" /> + <param name="samples" ftype="tsv" value="Samples.txt" /> + <param name="contrasts" ftype="tsv" value="Contrasts.txt" /> + <section name="adv"> + <param name="colgenes" value="3" /> + </section> + <section name="thresholds"> + <param name="th_cpm" value="10" /> + </section> + <output name="out_pdf" file="out.pdf" compare="sim_size"/> + <output name="output"> + <discovered_dataset designation="AskoAvsK" ftype="tsv" file="AskoAvsK.txt" compare="sim_size" /> + <discovered_dataset designation="AskoT1AvsT1K" ftype="tsv" file="AskoT1AvsT1K.txt" compare="sim_size" /> + <discovered_dataset designation="AskoT1vsT0" ftype="tsv" file="AskoT1vsT0.txt" compare="sim_size" /> + <discovered_dataset designation="AskoT1vsT2" ftype="tsv" file="AskoT1vsT2.txt" compare="sim_size" /> + <discovered_dataset designation="condition.asko" ftype="tsv" file="condition.asko.txt" compare="sim_size" /> + <discovered_dataset designation="context.asko" ftype="tsv" file="context.asko.txt" compare="sim_size" /> + <discovered_dataset designation="contrast.asko" ftype="tsv" file="contrast.asko.txt" compare="sim_size" /> + </output> + </test> + </tests> + <help><![CDATA[ +This tools generates a list of differential genes from various contrasts in an AskOmics format (https://askomics.github.io/). + +Example tabular input file of counts: + +============ ========== =============== =========== =========== ====== +miRNA read_count precursor total A32 A34 +------------ ---------- --------------- ----------- ----------- ------ +GL349623_679 346.00 GL349623_679 146.00 16.00 130.0 +GL349624_956 13.00 GL349624_956 13.00 0 13.0 +============ ========== =============== =========== =========== ====== + +Example tabular sample description file: + +============ ========== =============== =========== +ID condition stage treatment +------------ ---------- --------------- ----------- +A32 T3A T3 Acetone +A34 T3A T3 Acetone +============ ========== =============== =========== + +Example tabular contrast description file: + +============ ========================= ======================= +Contrast context1_of@Context context2_of@Context +------------ ------------------------- ----------------------- +T1vsT0 T1 T0 +T1vsT2 T1 T2 +============ ========================= ======================= + ]]></help> + <citations> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AskoAvsK.txt Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,176 @@ +Test_id measured_in@Contrast is@gene logFC FC PValue Expression Significance FDR A/T0A A/T1A A/T2A A/T3A K/T1K K/T2K K/T3K +AvsK_GL350151_32884 AvsK GL350151_32884 -1.4658015841445 2.76216898522126 0.00264391592225013 A=K 0 0.115671321598443 21.9770142082978 4.60243759106838 7.06858703220598 6.83597436231163 24.7243951164809 18.050368601277 19.5984932428693 +AvsK_GL350151_32898 AvsK GL350151_32898 -1.47172576071689 2.77353467197652 0.00240957402121667 A=K 0 0.115671321598443 22.8405187946568 4.60243759106838 7.06858703220598 7.18922297617649 25.6087427706126 18.2429383304036 20.3505714255447 +AvsK_GL350151_32906 AvsK GL350151_32906 -1.47172576071689 2.77353467197652 0.00240957402121667 A=K 0 0.115671321598443 22.8405187946568 4.60243759106838 7.06858703220598 7.18922297617649 25.6087427706126 18.2429383304036 20.3505714255447 +AvsK_GL351656_44862 AvsK GL351656_44862 -1.47172576071689 2.77353467197652 0.00240957402121667 A=K 0 0.115671321598443 22.8405187946568 4.60243759106838 7.06858703220598 7.18922297617649 25.6087427706126 18.2429383304036 20.3505714255447 +AvsK_GL349642_4945 AvsK GL349642_4945 -0.869495926967361 1.82702443243324 0.0200438004479275 A=K 0 0.157995720064168 417.507843046818 116.896489669693 101.61231882496 75.4079099203981 328.413968129475 202.836868768343 186.903274026939 +AvsK_GL349642_4959 AvsK GL349642_4959 -0.869495926967361 1.82702443243324 0.0200438004479275 A=K 0 0.157995720064168 417.507843046818 116.896489669693 101.61231882496 75.4079099203981 328.413968129475 202.836868768343 186.903274026939 +AvsK_GL349642_4961 AvsK GL349642_4961 -0.855495896450042 1.80938058523392 0.0222654184608194 A=K 0 0.157995720064168 82.6553684877643 26.2552964125283 20.5220334361146 16.7156895246482 69.0764764157016 45.5079252688433 35.4402876558247 +AvsK_GL349642_4963 AvsK GL349642_4963 -0.869495926967361 1.82702443243324 0.0200438004479275 A=K 0 0.157995720064168 417.507843046818 116.896489669693 101.61231882496 75.4079099203981 328.413968129475 202.836868768343 186.903274026939 +AvsK_GL349643_5190 AvsK GL349643_5190 -1.16487635288432 2.24213998375816 0.0150785191695021 A=K 0 0.157995720064168 14.4449688927881 2.73632941954876 4.84406512480566 2.93603778210461 11.030329473906 7.56335986023563 10.5777541213807 +AvsK_GL349773_18697 AvsK GL349773_18697 -0.91546742240643 1.8861800810935 0.00725049539559815 A=K 0 0.157995720064168 24.1677107608458 13.3933664191246 17.0744059570634 13.8406685924913 23.7616433874445 27.0937814638994 32.1556867228994 +AvsK_GL349919_26520 AvsK GL349919_26520 -0.566471255216122 1.48089695284404 0.0184409026827921 A=K 0 0.157995720064168 124.499541153818 72.073883410293 70.3745660356144 56.6307559204322 116.176752645774 101.682183109349 94.7831139445446 +AvsK_GL349919_26570 AvsK GL349919_26570 -0.978323108293458 1.97017407972835 0.0148075561063123 A=K 0 0.157995720064168 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+AvsK_api-mir-87a AvsK api-mir-87a -0.127723133034995 1.09256804473185 0.414280711984363 A=K 0 0.55342843204018 183.898246585246 359.274465229513 364.170268143297 516.851261150385 241.568668415364 336.035634591802 466.042315390537 +AvsK_api-mir-8 AvsK api-mir-8 -0.10201233232155 1.07326946078385 0.425615400913699 A=K 0 0.564262842120434 5301.5246677413 6852.54595327988 7719.78126352141 11054.9021049299 6234.11314807414 7208.95715011336 9613.89880962787 +AvsK_api-mir-263b AvsK api-mir-263b 0.277153919082733 1.21180193895981 0.460846748665548 A=K 0 0.606377300875721 1300.31895317557 1251.71642775122 1893.61155692519 1263.56130933943 994.460582209598 1337.23450831487 941.81504739292 +AvsK_GL349826_21746 AvsK GL349826_21746 -0.147020243200542 1.10728012119555 0.473495333788695 A=K 0 0.618370771738967 16.4951684939482 36.9544600878111 51.7665621942847 82.8005535132122 24.0458636715105 39.7552622980635 65.5617745846914 +AvsK_api-mir-3031 AvsK api-mir-3031 -0.157766270056588 1.11555857687433 0.477655932779107 A=K 0 0.619183616565509 197.60145077256 167.696215387838 173.378004991112 250.17481596556 188.245374819867 186.623430921134 226.185192350445 +AvsK_api-mir-100 AvsK api-mir-100 0.260596354979938 1.19797379885881 0.485071532886362 A=K 0 0.624172928346422 74.0061751109488 36.6867961405426 21.1027075981608 28.055245268287 37.0363811562773 30.2097239192629 18.5840373238262 +AvsK_GL350343_36473 AvsK GL350343_36473 -0.138637037764634 1.10086460085829 0.523836101000358 A=K 0 0.669133705657391 192.03628664115 162.229342389252 164.839570604831 240.375717813547 175.96217279623 180.069135472355 214.434156237149 +AvsK_api-bantam AvsK api-bantam 0.0736129017868095 1.05234875477952 0.540216462820689 A=K 0 0.683379789358212 13169.3308517045 16321.2717378554 17078.3447005196 21043.2913115408 12158.7515688539 14944.9044554132 18774.6570869758 +AvsK_api-mir-263a AvsK api-mir-263a 0.186426712885025 1.13794175263431 0.546703831486569 A=K 0 0.683379789358212 87248.5987485016 114738.540121811 163679.522376229 127221.007352086 94800.7276519968 115147.562359967 98013.8880180784 +AvsK_api-mir-2c AvsK api-mir-2c 0.0885690187666396 1.06331497771543 0.544984430369553 A=K 0 0.683379789358212 90.5431058071145 49.1092218181985 58.4232368367937 47.2771548685714 66.1195303451075 48.5029841502638 39.3961546589067 +AvsK_GL350370_36909 AvsK GL350370_36909 0.0911789334559931 1.06524031399593 0.586047582653191 A=K 0 0.727364021023464 547.199142865752 656.82657433825 772.848538093928 787.105725283942 458.154802585589 683.318052615232 657.046222558543 +AvsK_GL349650_6636 AvsK GL349650_6636 0.0802430481179375 1.05719612940176 0.628840531912338 A=K 0 0.748619680848022 571.761575450836 687.359529366427 806.208552002674 826.018496937716 484.997109051297 718.499068558673 692.399281998023 +AvsK_GL349650_6638 AvsK GL349650_6638 0.0802430481179375 1.05719612940176 0.628840531912338 A=K 0 0.748619680848022 571.761575450836 687.359529366427 806.208552002674 826.018496937716 484.997109051297 718.499068558673 692.399281998023 +AvsK_GL349650_6640 AvsK GL349650_6640 0.0802430481179375 1.05719612940176 0.628840531912338 A=K 0 0.748619680848022 571.761575450836 687.359529366427 806.208552002674 826.018496937716 484.997109051297 718.499068558673 692.399281998023 +AvsK_GL349650_6646 AvsK GL349650_6646 0.0802430481179375 1.05719612940176 0.628840531912338 A=K 0 0.748619680848022 571.761575450836 687.359529366427 806.208552002674 826.018496937716 484.997109051297 718.499068558673 692.399281998023 +AvsK_GL355572_46131 AvsK GL355572_46131 0.0803242676485381 1.05725564814132 0.628504627422985 A=K 0 0.748619680848022 571.761575450836 687.359529366427 806.389998999727 826.018496937716 484.997109051297 718.499068558673 692.399281998023 +AvsK_api-mir-317 AvsK api-mir-317 -0.105717384395713 1.0760293162243 0.622215874512894 A=K 0 0.748619680848022 38.1499577028816 41.9865638867419 43.1237487603943 81.4021479991145 39.973195910454 44.9959227533424 61.5132597451309 +AvsK_api-mir-137 AvsK api-mir-137 -0.123423899108211 1.08931703632151 0.64119056519725 A=K 0 0.758164519658911 23.3256938026282 31.1024416700597 32.0583379127441 39.3403084508284 30.2080451857782 33.5626380393697 29.7395236165053 +AvsK_api-mir-190 AvsK api-mir-190 0.0806722835198438 1.05751071668825 0.655611014523643 A=K 0 0.76487951694425 231.485466971721 234.550188295047 231.694995089182 220.167833553487 221.766347279128 205.845854702742 171.864204370512 +AvsK_api-mir-279b AvsK api-mir-279b 0.0513716604797051 1.03624968306798 0.654652121960051 A=K 0 0.76487951694425 626.144650512871 615.057540608426 593.854328320924 671.272152658071 554.283861464607 552.982505836701 560.625523157426 +AvsK_api-mir-3047-1 AvsK api-mir-3047-1 0.151069456771096 1.11039229080738 0.670395813232308 A=K 0 0.766792596834339 345.919356459137 203.230252972802 183.833264399272 170.686973097782 205.085416847614 179.143594709771 159.095755942028 +AvsK_api-mir-3047-2 AvsK api-mir-3047-2 0.151069456771096 1.11039229080738 0.670395813232308 A=K 0 0.766792596834339 345.919356459137 203.230252972802 183.833264399272 170.686973097782 205.085416847614 179.143594709771 159.095755942028 +AvsK_api-mir-3049 AvsK api-mir-3049 -0.0923073047951378 1.06607379354737 0.667230414901589 A=K 0 0.766792596834339 30.8771272639274 94.7105661640103 109.554845586267 96.9128255037697 53.1156765046011 72.0853763631651 100.188228378663 +AvsK_api-mir-276 AvsK api-mir-276 -0.0528175051643496 1.03728871562034 0.690826797354128 A=K 0 0.779965738948209 32203.6878048661 44732.2556555246 49739.6581555238 63483.937709086 36053.6225796423 47461.596670029 56999.0730502219 +AvsK_api-mir-3018 AvsK api-mir-3018 0.102779148361924 1.0738400727099 0.689427311952142 A=K 0 0.779965738948209 12.9763124689112 25.0073508370315 30.3840920325039 46.7376754442553 8.62911781908716 31.7226039874993 35.7693923336448 +AvsK_api-mir-3032 AvsK api-mir-3032 -0.100105200009885 1.07185161813161 0.705438761882478 A=K 0 0.791357585445087 77.401034703635 31.6881532348652 23.4780389246877 15.7470662528429 36.4674445149938 32.8486087182833 22.7343341312668 +AvsK_api-mir-3027 AvsK api-mir-3027 0.0697520221921975 1.04953626845249 0.713779269627093 A=K 0 0.795613835571601 492.94034451663 404.312998546403 373.591616924324 451.239789489599 362.527824297402 382.300123100955 381.724605218335 +AvsK_api-mir-993 AvsK api-mir-993 0.0438223818466387 1.03084139840492 0.742855650107538 A=K 0 0.822783156764678 364.184068355389 517.095986431029 451.118742022456 402.660704268363 355.927103464731 417.649465514703 379.069596290388 +AvsK_api-mir-9b AvsK api-mir-9b 0.0385033971553266 1.02704784928473 0.783762109394139 A=K 0 0.862631252477826 376.361439667079 436.573003510837 398.350992944513 415.493971885812 335.799016629453 364.731785016796 391.941058078227 +AvsK_api-mir-34 AvsK api-mir-34 -0.047003921762674 1.03311719606348 0.799312897918059 A=K 0 0.874248482097877 33.78320785053 33.6733146899426 36.5841102943991 75.4315901355026 26.767434430309 37.427678364582 62.5278754461016 +AvsK_api-mir-3016 AvsK api-mir-3016 0.0708655877421499 1.05034668130115 0.826909647602724 A=K 0 0.898814834350787 31.184883216559 10.4497505123629 5.33918096274054 5.83303583149121 21.1433464017102 5.2451550522054 5.31862877995631 +AvsK_GL349801_20413 AvsK GL349801_20413 0.0435856177678198 1.03067223847775 0.862187240266329 A=K 0 0.912423580011872 18.9258171290887 19.7476856197604 15.6293738213989 18.2029055558623 14.9856656593161 15.2885918081573 16.7328814031433 +AvsK_api-mir-252b AvsK api-mir-252b -0.0432783324776981 1.03045273492187 0.872564637171943 A=K 0 0.912423580011872 70.3219832837863 80.5998452829956 87.3965220353206 133.122575098307 66.0945308776993 89.0590652091734 105.469416792266 +AvsK_api-mir-277 AvsK api-mir-277 0.0214744928271797 1.014996317245 0.886881773510312 A=K 0 0.912423580011872 74.0187227137694 95.8454418109413 101.094878069469 138.38081811116 59.950707904155 93.4734733070941 124.973319561987 +AvsK_api-mir-29 AvsK api-mir-29 0.0273401385118148 1.01913144489008 0.890832263031452 A=K 0 0.912423580011872 107.910313729097 105.245364266731 98.7017420713852 79.8792663335928 94.6171458451392 94.9590209808936 72.2709794245771 +AvsK_api-mir-3036-1 AvsK api-mir-3036-1 -0.0233521058686877 1.01631815654608 0.890603796414289 A=K 0 0.912423580011872 468.48378934247 355.864419414785 375.340801378356 389.66489521967 378.098568231729 371.431717521057 358.320995881957 +AvsK_api-mir-3036-2 AvsK api-mir-3036-2 -0.0233521058686877 1.01631815654608 0.890603796414289 A=K 0 0.912423580011872 468.48378934247 355.864419414785 375.340801378356 389.66489521967 378.098568231729 371.431717521057 358.320995881957 +AvsK_api-mir-3036-3 AvsK api-mir-3036-3 -0.0231499688035336 1.01617576943556 0.891568183897315 A=K 0 0.912423580011872 468.48378934247 356.02291302258 375.157547119293 389.66489521967 377.932084361907 371.431717521057 358.320995881957 +AvsK_api-mir-3036-4 AvsK api-mir-3036-4 -0.0231499688035336 1.01617576943556 0.891568183897315 A=K 0 0.912423580011872 468.48378934247 356.02291302258 375.157547119293 389.66489521967 377.932084361907 371.431717521057 358.320995881957 +AvsK_api-mir-3036-5 AvsK api-mir-3036-5 -0.0231499688035336 1.01617576943556 0.891568183897315 A=K 0 0.912423580011872 468.48378934247 356.02291302258 375.157547119293 389.66489521967 377.932084361907 371.431717521057 358.320995881957 +AvsK_api-mir-9a AvsK api-mir-9a -0.0283397691516339 1.01983783675679 0.848692896454689 A=K 0 0.912423580011872 841.300362032995 812.438450656032 879.112275743298 1109.15485486028 786.952021519981 819.629737700813 961.930573546304 +AvsK_api-mir-7 AvsK api-mir-7 -0.028830626121343 1.02018488146532 0.901282950260523 A=K 0 0.917003001718556 192.866444597218 181.345502480794 207.034028814017 198.912796525837 189.343819213867 173.186336148056 186.872702427546 +AvsK_api-mir-3043-1 AvsK api-mir-3043-1 -0.047426737362225 1.03342001964741 0.925825733899933 A=K 0 0.925825733899933 50.1296395288814 57.6997552376986 48.3999867820141 44.4558265605947 40.4424775820102 51.5082654013472 48.4219380775634 +AvsK_api-mir-3043-2 AvsK api-mir-3043-2 -0.047426737362225 1.03342001964741 0.925825733899933 A=K 0 0.925825733899933 50.1296395288814 57.6997552376986 48.3999867820141 44.4558265605947 40.4424775820102 51.5082654013472 48.4219380775634 +AvsK_api-mir-3043-3 AvsK api-mir-3043-3 -0.047426737362225 1.03342001964741 0.925825733899933 A=K 0 0.925825733899933 50.1296395288814 57.6997552376986 48.3999867820141 44.4558265605947 40.4424775820102 51.5082654013472 48.4219380775634
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AskoT1AvsT1K.txt Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,176 @@ +Test_id measured_in@Contrast is@gene logFC FC PValue Expression Significance FDR T1A/T1A T1K/T1K +T1AvsT1K_GL349642_4945 T1AvsT1K GL349642_4945 -1.51050082924554 2.84908927626456 0.0325406523649849 T1A=T1K 0 0.226146729807717 116.896489669693 328.413968129475 +T1AvsT1K_GL349642_4959 T1AvsT1K GL349642_4959 -1.51050082924554 2.84908927626456 0.0325406523649849 T1A=T1K 0 0.226146729807717 116.896489669693 328.413968129475 +T1AvsT1K_GL349642_4963 T1AvsT1K GL349642_4963 -1.51050082924554 2.84908927626456 0.0325406523649849 T1A=T1K 0 0.226146729807717 116.896489669693 328.413968129475 +T1AvsT1K_GL349642_4967 T1AvsT1K GL349642_4967 -1.97373986469 3.92785007847171 0.0258331015676455 T1A=T1K 0 0.226146729807717 6.64462795004153 25.6873101470662 +T1AvsT1K_GL349643_5180 T1AvsT1K GL349643_5180 -2.03033393204775 4.08499392267698 0.0235010575102647 T1A=T1K 0 0.226146729807717 4.54212254256334 17.4668387068677 +T1AvsT1K_GL349643_5182 T1AvsT1K GL349643_5182 -2.05332502278382 4.15061472722808 0.025644995276629 T1A=T1K 0 0.226146729807717 4.31590876285712 16.8703162971331 +T1AvsT1K_GL349643_5190 T1AvsT1K GL349643_5190 -2.10030669556043 4.28800531956913 0.0200142821918946 T1A=T1K 0 0.226146729807717 2.73632941954876 11.030329473906 +T1AvsT1K_GL349645_5442 T1AvsT1K GL349645_5442 -1.86137255910447 3.6335318668081 0.0328569344298816 T1A=T1K 0 0.226146729807717 14.8582519250457 52.996163581116 +T1AvsT1K_GL349919_26570 T1AvsT1K GL349919_26570 -1.82005151771302 3.53093807044136 0.0177844713678188 T1A=T1K 0 0.226146729807717 25.4501089849405 87.6001270254807 +T1AvsT1K_GL349919_26592 T1AvsT1K GL349919_26592 -2.04867364035024 4.1372543101038 0.0335989427142894 T1A=T1K 0 0.226146729807717 6.67628355694396 25.3243219280574 +T1AvsT1K_GL350151_32862 T1AvsT1K GL350151_32862 -1.60518545010683 3.0423485576661 0.0196696225009638 T1A=T1K 0 0.226146729807717 29.3696377720969 86.6672382227376 +T1AvsT1K_GL350151_32866 T1AvsT1K GL350151_32866 -1.61402230907525 3.06104087360107 0.02011994144567 T1A=T1K 0 0.226146729807717 29.8894059094906 88.817436670779 +T1AvsT1K_GL350151_32884 T1AvsT1K GL350151_32884 -2.49624962959045 5.64216802207781 0.00756439706040851 T1A=T1K 0 0.226146729807717 4.60243759106838 24.7243951164809 +T1AvsT1K_GL350151_32890 T1AvsT1K GL350151_32890 -1.35097712821537 2.55084834312908 0.0300022327131185 T1A=T1K 0 0.226146729807717 17.5104113748143 42.2838873109649 +T1AvsT1K_GL350151_32898 T1AvsT1K GL350151_32898 -2.54430493829757 5.83327034653207 0.00640778257543885 T1A=T1K 0 0.226146729807717 4.60243759106838 25.6087427706126 +T1AvsT1K_GL350151_32906 T1AvsT1K GL350151_32906 -2.54430493829757 5.83327034653207 0.00640778257543885 T1A=T1K 0 0.226146729807717 4.60243759106838 25.6087427706126 +T1AvsT1K_GL350151_32910 T1AvsT1K GL350151_32910 -1.35369228094108 2.55565356116857 0.0275501325768629 T1A=T1K 0 0.226146729807717 17.7366251545205 42.92724866839 +T1AvsT1K_GL350737_41242 T1AvsT1K GL350737_41242 -1.35369228094108 2.55565356116857 0.0275501325768629 T1A=T1K 0 0.226146729807717 17.7366251545205 42.92724866839 +T1AvsT1K_GL351656_44862 T1AvsT1K GL351656_44862 -2.54430493829757 5.83327034653207 0.00640778257543885 T1A=T1K 0 0.226146729807717 4.60243759106838 25.6087427706126 +T1AvsT1K_GL366836_47437 T1AvsT1K GL366836_47437 -1.97373986469 3.92785007847171 0.0258331015676455 T1A=T1K 0 0.226146729807717 6.64462795004153 25.6873101470662 +T1AvsT1K_GL366836_47447 T1AvsT1K GL366836_47447 -1.97373986469 3.92785007847171 0.0258331015676455 T1A=T1K 0 0.226146729807717 6.64462795004153 25.6873101470662 +T1AvsT1K_api-mir-210 T1AvsT1K api-mir-210 1.07892833969205 2.11246631948654 0.0166401855616645 T1A=T1K 0 0.226146729807717 45.7488925668745 20.0195697686999 +T1AvsT1K_api-mir-252a T1AvsT1K api-mir-252a 0.771658396805771 1.70723114052703 0.0131086796680285 T1A=T1K 0 0.226146729807717 489.114196700038 289.171809924299 +T1AvsT1K_api-mir-277 T1AvsT1K api-mir-277 0.66530286763414 1.58590116943775 0.0271266048425514 T1A=T1K 0 0.226146729807717 95.8454418109413 59.950707904155 +T1AvsT1K_api-mir-3018 T1AvsT1K api-mir-3018 1.46695527580135 2.76437871473862 0.00721009463641135 T1A=T1K 0 0.226146729807717 25.0073508370315 8.62911781908716 +T1AvsT1K_api-mir-3033 T1AvsT1K api-mir-3033 0.590231469947568 1.50548827270089 0.0118480303953249 T1A=T1K 0 0.226146729807717 502.552807518651 332.193472624891 +T1AvsT1K_api-mir-3049 T1AvsT1K api-mir-3049 0.885259979868827 1.84709744639616 0.0366479961472712 T1A=T1K 0 0.229049975920445 94.7105661640103 53.1156765046011 +T1AvsT1K_api-mir-993 T1AvsT1K api-mir-993 0.548062229485617 1.4621205144276 0.0355545728873468 T1A=T1K 0 0.229049975920445 517.095986431029 355.927103464731 +T1AvsT1K_GL349630_2419 T1AvsT1K GL349630_2419 -1.49476035124183 2.81817333938257 0.0615172803842476 T1A=T1K 0 0.231296705500048 40.7692899051509 112.352482308845 +T1AvsT1K_GL349630_2421 T1AvsT1K GL349630_2421 -1.49476035124183 2.81817333938257 0.0615172803842476 T1A=T1K 0 0.231296705500048 40.7692899051509 112.352482308845 +T1AvsT1K_GL349630_2423 T1AvsT1K GL349630_2423 -1.49476035124183 2.81817333938257 0.0615172803842476 T1A=T1K 0 0.231296705500048 40.7692899051509 112.352482308845 +T1AvsT1K_GL349630_2425 T1AvsT1K GL349630_2425 -1.49476035124183 2.81817333938257 0.0615172803842476 T1A=T1K 0 0.231296705500048 40.7692899051509 112.352482308845 +T1AvsT1K_GL349630_2427 T1AvsT1K GL349630_2427 -2.16541513820586 4.48595496837273 0.0735177899692301 T1A=T1K 0 0.231296705500048 3.31343434155413 13.0513763298296 +T1AvsT1K_GL349642_4947 T1AvsT1K GL349642_4947 -1.23593995097064 2.35534754095378 0.122917677780026 T1A=T1K 0 0.231296705500048 10.8735388983366 23.3733601863652 +T1AvsT1K_GL349642_4949 T1AvsT1K GL349642_4949 -1.63035664942331 3.09589523043133 0.0884603313800414 T1A=T1K 0 0.231296705500048 6.08975436654529 16.9645086841215 +T1AvsT1K_GL349642_4951 T1AvsT1K GL349642_4951 -1.23593995097064 2.35534754095378 0.122917677780026 T1A=T1K 0 0.231296705500048 10.8735388983366 23.3733601863652 +T1AvsT1K_GL349642_4954 T1AvsT1K GL349642_4954 -1.33431476298014 2.52155686905087 0.110903579806168 T1A=T1K 0 0.231296705500048 65.6308127111902 161.027468412219 +T1AvsT1K_GL349642_4955 T1AvsT1K GL349642_4955 -1.23593995097064 2.35534754095378 0.122917677780026 T1A=T1K 0 0.231296705500048 10.8735388983366 23.3733601863652 +T1AvsT1K_GL349642_4958 T1AvsT1K GL349642_4958 -1.33431476298014 2.52155686905087 0.110903579806168 T1A=T1K 0 0.231296705500048 65.6308127111902 161.027468412219 +T1AvsT1K_GL349642_4961 T1AvsT1K GL349642_4961 -1.42321928473895 2.68183278164377 0.0413841103723519 T1A=T1K 0 0.231296705500048 26.2552964125283 69.0764764157016 +T1AvsT1K_GL349642_4965 T1AvsT1K GL349642_4965 -1.23593995097064 2.35534754095378 0.122917677780026 T1A=T1K 0 0.231296705500048 10.8735388983366 23.3733601863652 +T1AvsT1K_GL349642_4972 T1AvsT1K GL349642_4972 -1.33431476298014 2.52155686905087 0.110903579806168 T1A=T1K 0 0.231296705500048 65.6308127111902 161.027468412219 +T1AvsT1K_GL349642_4974 T1AvsT1K GL349642_4974 -1.35764348199695 2.56266248632493 0.10494283327168 T1A=T1K 0 0.231296705500048 53.3370100028057 132.896009310663 +T1AvsT1K_GL349642_4976 T1AvsT1K GL349642_4976 -1.33431476298014 2.52155686905087 0.110903579806168 T1A=T1K 0 0.231296705500048 65.6308127111902 161.027468412219 +T1AvsT1K_GL349642_4978 T1AvsT1K GL349642_4978 -1.34474630664066 2.53985530028607 0.109696804426897 T1A=T1K 0 0.231296705500048 60.807187993068 150.137655781385 +T1AvsT1K_GL349642_4980 T1AvsT1K GL349642_4980 -1.33431476298014 2.52155686905087 0.110903579806168 T1A=T1K 0 0.231296705500048 65.6308127111902 161.027468412219 +T1AvsT1K_GL349642_4982 T1AvsT1K GL349642_4982 -1.35764348199695 2.56266248632493 0.10494283327168 T1A=T1K 0 0.231296705500048 53.3370100028057 132.896009310663 +T1AvsT1K_GL349645_5438 T1AvsT1K GL349645_5438 -1.54550599726022 2.91906431406472 0.0767362953308844 T1A=T1K 0 0.231296705500048 14.9720786249046 42.2540174631687 +T1AvsT1K_GL349645_5440 T1AvsT1K GL349645_5440 -1.54550599726022 2.91906431406472 0.0767362953308844 T1A=T1K 0 0.231296705500048 14.9720786249046 42.2540174631687 +T1AvsT1K_GL349645_5448 T1AvsT1K GL349645_5448 -1.75574713222178 3.37701159350507 0.0472151079231076 T1A=T1K 0 0.231296705500048 20.234881500788 66.9746615631992 +T1AvsT1K_GL349645_5452 T1AvsT1K GL349645_5452 -1.54550599726022 2.91906431406472 0.0767362953308844 T1A=T1K 0 0.231296705500048 14.9720786249046 42.2540174631687 +T1AvsT1K_GL349645_5454 T1AvsT1K GL349645_5454 -1.75574713222178 3.37701159350507 0.0472151079231076 T1A=T1K 0 0.231296705500048 20.234881500788 66.9746615631992 +T1AvsT1K_GL349650_6636 T1AvsT1K GL349650_6636 0.497833165795097 1.41209109979762 0.116069852418871 T1A=T1K 0 0.231296705500048 687.359529366427 484.997109051297 +T1AvsT1K_GL349650_6638 T1AvsT1K GL349650_6638 0.497833165795097 1.41209109979762 0.116069852418871 T1A=T1K 0 0.231296705500048 687.359529366427 484.997109051297 +T1AvsT1K_GL349650_6640 T1AvsT1K GL349650_6640 0.497833165795097 1.41209109979762 0.116069852418871 T1A=T1K 0 0.231296705500048 687.359529366427 484.997109051297 +T1AvsT1K_GL349650_6646 T1AvsT1K GL349650_6646 0.497833165795097 1.41209109979762 0.116069852418871 T1A=T1K 0 0.231296705500048 687.359529366427 484.997109051297 +T1AvsT1K_GL349742_15837 T1AvsT1K GL349742_15837 0.411244414495148 1.32983238294201 0.070181507649193 T1A=T1K 0 0.231296705500048 16838.4837907878 12660.4383260529 +T1AvsT1K_GL349755_17087 T1AvsT1K GL349755_17087 -2.16541513820586 4.48595496837273 0.0735177899692301 T1A=T1K 0 0.231296705500048 3.31343434155413 13.0513763298296 +T1AvsT1K_GL349773_18697 T1AvsT1K GL349773_18697 -0.968466218438465 1.95675918711029 0.113974718044555 T1A=T1K 0 0.231296705500048 13.3933664191246 23.7616433874445 +T1AvsT1K_GL349919_26520 T1AvsT1K GL349919_26520 -0.704438668191757 1.62951052243089 0.107905899082826 T1A=T1K 0 0.231296705500048 72.073883410293 116.176752645774 +T1AvsT1K_GL349919_26542 T1AvsT1K GL349919_26542 -1.89967113071637 3.73128130564866 0.0553127380658989 T1A=T1K 0 0.231296705500048 24.4503049468148 89.0011005229108 +T1AvsT1K_GL349919_26564 T1AvsT1K GL349919_26564 -1.89967113071637 3.73128130564866 0.0553127380658989 T1A=T1K 0 0.231296705500048 24.4503049468148 89.0011005229108 +T1AvsT1K_GL349919_26580 T1AvsT1K GL349919_26580 -1.88830973574709 3.70201242099229 0.0543571474967192 T1A=T1K 0 0.231296705500048 24.4503049468148 88.2849331910451 +T1AvsT1K_GL349919_26590 T1AvsT1K GL349919_26590 -1.89967113071637 3.73128130564866 0.0553127380658989 T1A=T1K 0 0.231296705500048 24.4503049468148 89.0011005229108 +T1AvsT1K_GL350151_32870 T1AvsT1K GL350151_32870 -1.71142129674047 3.27483290557102 0.070666140324755 T1A=T1K 0 0.231296705500048 6.52577459753034 20.259888596177 +T1AvsT1K_GL350151_32872 T1AvsT1K GL350151_32872 -1.29385258523086 2.45181918009994 0.0777523367711501 T1A=T1K 0 0.231296705500048 17.422074847417 40.2506014278924 +T1AvsT1K_GL350151_32913 T1AvsT1K GL350151_32913 -1.80016728732826 3.48260605445201 0.0927363069708863 T1A=T1K 0 0.231296705500048 4.66115555795739 16.0514731430306 +T1AvsT1K_GL350151_32915 T1AvsT1K GL350151_32915 -1.80016728732826 3.48260605445201 0.0927363069708863 T1A=T1K 0 0.231296705500048 4.66115555795739 16.0514731430306 +T1AvsT1K_GL350370_36909 T1AvsT1K GL350370_36909 0.513809574434009 1.42781550567439 0.10797209488329 T1A=T1K 0 0.231296705500048 656.82657433825 458.154802585589 +T1AvsT1K_GL350677_40695 T1AvsT1K GL350677_40695 -1.43317141992196 2.70039681026893 0.0901034620644428 T1A=T1K 0 0.231296705500048 5.6136940181826 13.8990465055077 +T1AvsT1K_GL350682_40710 T1AvsT1K GL350682_40710 -2.15046864545504 4.43971985387644 0.108767381438483 T1A=T1K 0 0.231296705500048 11.8785246839619 57.6693961245775 +T1AvsT1K_GL350737_41243 T1AvsT1K GL350737_41243 -1.80016728732826 3.48260605445201 0.0927363069708863 T1A=T1K 0 0.231296705500048 4.66115555795739 16.0514731430306 +T1AvsT1K_GL351656_44870 T1AvsT1K GL351656_44870 -1.81026708625766 3.50707208972786 0.0521068788795251 T1A=T1K 0 0.231296705500048 28.7778527542278 98.2409625950879 +T1AvsT1K_GL355572_46131 T1AvsT1K GL355572_46131 0.49783313065797 1.41209106540586 0.116079251254069 T1A=T1K 0 0.231296705500048 687.359529366427 484.997109051297 +T1AvsT1K_GL357043_46322 T1AvsT1K GL357043_46322 -2.16541513820586 4.48595496837273 0.0735177899692301 T1A=T1K 0 0.231296705500048 3.31343434155413 13.0513763298296 +T1AvsT1K_GL366836_47443 T1AvsT1K GL366836_47443 -1.63035664942331 3.09589523043133 0.0884603313800414 T1A=T1K 0 0.231296705500048 6.08975436654529 16.9645086841215 +T1AvsT1K_GL369698_47842 T1AvsT1K GL369698_47842 -1.80016728732826 3.48260605445201 0.0927363069708863 T1A=T1K 0 0.231296705500048 4.66115555795739 16.0514731430306 +T1AvsT1K_GL369698_47844 T1AvsT1K GL369698_47844 -1.80016728732826 3.48260605445201 0.0927363069708863 T1A=T1K 0 0.231296705500048 4.66115555795739 16.0514731430306 +T1AvsT1K_api-bantam T1AvsT1K api-bantam 0.424998755736059 1.34257134486831 0.0655686813955212 T1A=T1K 0 0.231296705500048 16321.2717378554 12158.7515688539 +T1AvsT1K_api-mir-279a T1AvsT1K api-mir-279a 0.351334886816963 1.27574048966057 0.0815425644557342 T1A=T1K 0 0.231296705500048 1807.69888237487 1417.07904547563 +T1AvsT1K_api-mir-2a T1AvsT1K api-mir-2a 0.437311522850856 1.35407863529223 0.092462956933114 T1A=T1K 0 0.231296705500048 1126.12814528614 834.523638972188 +T1AvsT1K_api-mir-3016 T1AvsT1K api-mir-3016 -1.02364303310583 2.03304624650033 0.0893446933132216 T1A=T1K 0 0.231296705500048 10.4497505123629 21.1433464017102 +T1AvsT1K_api-mir-3050 T1AvsT1K api-mir-3050 0.521983087561393 1.43592767741867 0.105153476136855 T1A=T1K 0 0.231296705500048 1142501.70015826 795661.911903157 +T1AvsT1K_api-mir-3055-1 T1AvsT1K api-mir-3055-1 -1.11623233737473 2.16780101691872 0.122735999369461 T1A=T1K 0 0.231296705500048 18.2112883523139 38.1421525702081 +T1AvsT1K_api-mir-3055-2 T1AvsT1K api-mir-3055-2 -1.11623233737473 2.16780101691872 0.122735999369461 T1A=T1K 0 0.231296705500048 18.2112883523139 38.1421525702081 +T1AvsT1K_api-mir-3055-3 T1AvsT1K api-mir-3055-3 -1.11623233737473 2.16780101691872 0.122735999369461 T1A=T1K 0 0.231296705500048 18.2112883523139 38.1421525702081 +T1AvsT1K_api-mir-3055-4 T1AvsT1K api-mir-3055-4 -1.11623233737473 2.16780101691872 0.122735999369461 T1A=T1K 0 0.231296705500048 18.2112883523139 38.1421525702081 +T1AvsT1K_api-mir-3055-5 T1AvsT1K api-mir-3055-5 -1.11623233737473 2.16780101691872 0.122735999369461 T1A=T1K 0 0.231296705500048 18.2112883523139 38.1421525702081 +T1AvsT1K_api-mir-316 T1AvsT1K api-mir-316 0.951214903067856 1.93350018581491 0.0534469540017206 T1A=T1K 0 0.231296705500048 29.2940452013454 14.9534399843751 +T1AvsT1K_api-mir-87a T1AvsT1K api-mir-87a 0.595075684837031 1.51055182813797 0.0499574684537706 T1A=T1K 0 0.231296705500048 359.274465229513 241.568668415364 +T1AvsT1K_api-mir-927 T1AvsT1K api-mir-927 0.720303478899567 1.64752856485343 0.0622009899327027 T1A=T1K 0 0.231296705500048 1222.6871883341 742.960038441659 +T1AvsT1K_api-mir-929 T1AvsT1K api-mir-929 0.586766004331637 1.50187631270286 0.121743465161997 T1A=T1K 0 0.231296705500048 45.7383427423633 30.9159434838904 +T1AvsT1K_api-mir-996 T1AvsT1K api-mir-996 0.927303324713245 1.90171799410889 0.116083317468116 T1A=T1K 0 0.231296705500048 30.9540188931113 16.9072732178458 +T1AvsT1K_api-mir-315 T1AvsT1K api-mir-315 0.374266854283351 1.29618069688973 0.129025414693314 T1A=T1K 0 0.240206889056702 20928.2550507448 16149.5398678988 +T1AvsT1K_api-mir-184a T1AvsT1K api-mir-184a 0.449003737181593 1.36509725405156 0.136775487455678 T1A=T1K 0 0.250429142868427 48955.440785817 35866.6670300699 +T1AvsT1K_api-mir-3040 T1AvsT1K api-mir-3040 0.526844003267613 1.4407739514075 0.137378272659252 T1A=T1K 0 0.250429142868427 461.832106680395 318.572656659124 +T1AvsT1K_GL349826_21746 T1AvsT1K GL349826_21746 0.582768141488699 1.49772021336045 0.140133693798645 T1A=T1K 0 0.251872093496074 36.9544600878111 24.0458636715105 +T1AvsT1K_api-mir-2c T1AvsT1K api-mir-2c -0.406676759257996 1.32562871539024 0.142487641463493 T1A=T1K 0 0.251872093496074 49.1092218181985 66.1195303451075 +T1AvsT1K_api-mir-9b T1AvsT1K api-mir-9b 0.392950256241558 1.31307585012194 0.142275696189531 T1A=T1K 0 0.251872093496074 436.573003510837 335.799016629453 +T1AvsT1K_GL349642_4969 T1AvsT1K GL349642_4969 -1.49514213376617 2.81891921545201 0.152512110771756 T1A=T1K 0 0.257952551789253 6.55800972940896 16.178928282704 +T1AvsT1K_GL366836_47439 T1AvsT1K GL366836_47439 -1.49514213376617 2.81891921545201 0.152512110771756 T1A=T1K 0 0.257952551789253 6.55800972940896 16.178928282704 +T1AvsT1K_GL366836_47441 T1AvsT1K GL366836_47441 -1.49514213376617 2.81891921545201 0.152512110771756 T1A=T1K 0 0.257952551789253 6.55800972940896 16.178928282704 +T1AvsT1K_GL366836_47445 T1AvsT1K GL366836_47445 -1.49514213376617 2.81891921545201 0.152512110771756 T1A=T1K 0 0.257952551789253 6.55800972940896 16.178928282704 +T1AvsT1K_api-mir-3043-1 T1AvsT1K api-mir-3043-1 0.508740050687805 1.4228070723011 0.157719560236857 T1A=T1K 0 0.257952551789253 57.6997552376986 40.4424775820102 +T1AvsT1K_api-mir-3043-2 T1AvsT1K api-mir-3043-2 0.508740050687805 1.4228070723011 0.157719560236857 T1A=T1K 0 0.257952551789253 57.6997552376986 40.4424775820102 +T1AvsT1K_api-mir-3043-3 T1AvsT1K api-mir-3043-3 0.508740050687805 1.4228070723011 0.157719560236857 T1A=T1K 0 0.257952551789253 57.6997552376986 40.4424775820102 +T1AvsT1K_api-mir-71 T1AvsT1K api-mir-71 0.512248297414581 1.4262711669984 0.155004135916791 T1A=T1K 0 0.257952551789253 110.914522043777 77.5719375098147 +T1AvsT1K_api-mir-998 T1AvsT1K api-mir-998 0.307846346959952 1.2378584467283 0.165301748749579 T1A=T1K 0 0.267850055844225 35311.3030595825 28527.9229897474 +T1AvsT1K_GL350137_32551 T1AvsT1K GL350137_32551 -1.48556094305621 2.80026030583413 0.173104045541299 T1A=T1K 0 0.27791933917181 204.143997030395 578.995678143302 +T1AvsT1K_api-mir-184b T1AvsT1K api-mir-184b 0.400186589358911 1.31967857889766 0.195983594794627 T1A=T1K 0 0.311792082627815 43427.1191642789 32911.4007978194 +T1AvsT1K_api-mir-306 T1AvsT1K api-mir-306 0.257397955103677 1.19532087843988 0.205380357103338 T1A=T1K 0 0.323797860298055 1764.58022199887 1478.63566622894 +T1AvsT1K_api-mir-276 T1AvsT1K api-mir-276 0.311354966929614 1.24087256981427 0.215100871481478 T1A=T1K 0 0.33609511168981 44732.2556555246 36053.6225796423 +T1AvsT1K_api-mir-10 T1AvsT1K api-mir-10 0.57454860954382 1.48921144571279 0.219566827241792 T1A=T1K 0 0.336716196969914 1609762.52422668 1080955.87403039 +T1AvsT1K_api-mir-92a-1 T1AvsT1K api-mir-92a-1 0.420513679344852 1.33840401592113 0.221270643723087 T1A=T1K 0 0.336716196969914 72.386227867033 54.1490720179198 +T1AvsT1K_api-mir-92a-2 T1AvsT1K api-mir-92a-2 0.420513679344852 1.33840401592113 0.221270643723087 T1A=T1K 0 0.336716196969914 72.386227867033 54.1490720179198 +T1AvsT1K_api-mir-87b T1AvsT1K api-mir-87b 0.417330099248798 1.33545383001126 0.233533965033266 T1A=T1K 0 0.352314171386393 178.020931797068 136.169251352098 +T1AvsT1K_api-mir-34 T1AvsT1K api-mir-34 0.413664958815808 1.3320654398123 0.239095482482801 T1A=T1K 0 0.357621448158036 33.6733146899426 26.767434430309 +T1AvsT1K_GL349872_24254 T1AvsT1K GL349872_24254 0.26580802408479 1.20230924988958 0.245895974243057 T1A=T1K 0 0.364676232987585 732.301073986264 610.570405139264 +T1AvsT1K_api-mir-275 T1AvsT1K api-mir-275 -0.502466168303267 1.41663311135617 0.248333218933857 T1A=T1K 0 0.365195910196848 53.5416861018258 80.9148205341786 +T1AvsT1K_GL349928_26838 T1AvsT1K GL349928_26838 0.398368230595902 1.31801631665353 0.252691639408594 T1A=T1K 0 0.3685086408042 48.4496831345842 38.5345853531023 +T1AvsT1K_GL350137_32552 T1AvsT1K GL350137_32552 -1.22471269108503 2.33708902565558 0.259667178176632 T1A=T1K 0 0.372473411318939 116.544493511701 279.125976791414 +T1AvsT1K_GL350468_38246 T1AvsT1K GL350468_38246 0.407728640758765 1.32659559525244 0.2592622601322 T1A=T1K 0 0.372473411318939 683.497118292956 521.57331291497 +T1AvsT1K_api-mir-2b T1AvsT1K api-mir-2b 0.262550179111588 1.19959729912042 0.324723486955096 T1A=T1K 0 0.462004961114974 532.896316982273 446.401152061298 +T1AvsT1K_GL349801_20413 T1AvsT1K GL349801_20413 0.451502682632779 1.36746383853809 0.355270554276646 T1A=T1K 0 0.501389895148492 19.7476856197604 14.9856656593161 +T1AvsT1K_api-mir-281 T1AvsT1K api-mir-281 0.476202790276553 1.39107749270099 0.363742343549682 T1A=T1K 0 0.509239280969554 17.9980028180635 14.6499713109873 +T1AvsT1K_GL350757_41318 T1AvsT1K GL350757_41318 0.246282640996919 1.18614685682722 0.41532759271975 T1A=T1K 0 0.55482693683936 154.093033384431 133.130797853428 +T1AvsT1K_GL350757_41320 T1AvsT1K GL350757_41320 0.246282640996919 1.18614685682722 0.41532759271975 T1A=T1K 0 0.55482693683936 154.093033384431 133.130797853428 +T1AvsT1K_GL350757_41322 T1AvsT1K GL350757_41322 0.246282640996919 1.18614685682722 0.41532759271975 T1A=T1K 0 0.55482693683936 154.093033384431 133.130797853428 +T1AvsT1K_GL350757_41324 T1AvsT1K GL350757_41324 0.246282640996919 1.18614685682722 0.41532759271975 T1A=T1K 0 0.55482693683936 154.093033384431 133.130797853428 +T1AvsT1K_GL350757_41326 T1AvsT1K GL350757_41326 0.246282640996919 1.18614685682722 0.41532759271975 T1A=T1K 0 0.55482693683936 154.093033384431 133.130797853428 +T1AvsT1K_GL350757_41328 T1AvsT1K GL350757_41328 0.246282640996919 1.18614685682722 0.41532759271975 T1A=T1K 0 0.55482693683936 154.093033384431 133.130797853428 +T1AvsT1K_api-mir-14 T1AvsT1K api-mir-14 0.2596082631212 1.19715359579451 0.455207762811824 T1A=T1K 0 0.603495140091434 5174.26337501864 4324.71028742041 +T1AvsT1K_api-mir-279b T1AvsT1K api-mir-279b 0.152154812957104 1.11122796609104 0.47830843605556 T1A=T1K 0 0.629353205336263 615.057540608426 554.283861464607 +T1AvsT1K_api-mir-252b T1AvsT1K api-mir-252b 0.356436208575587 1.28025945040909 0.482876581824342 T1A=T1K 0 0.630622401636268 80.5998452829956 66.0945308776993 +T1AvsT1K_GL349650_6642 T1AvsT1K GL349650_6642 -0.272750292181644 1.20810872067623 0.503308619702765 T1A=T1K 0 0.652437099614695 19.27700657408 23.4204958217444 +T1AvsT1K_api-mir-3041 T1AvsT1K api-mir-3041 0.24650120531014 1.18632656841183 0.511596497306279 T1A=T1K 0 0.658304316386756 83.1697934295355 68.7196716946604 +T1AvsT1K_GL349650_6644 T1AvsT1K GL349650_6644 -0.245638478191897 1.18561736091067 0.522084683127115 T1A=T1K 0 0.666896493045585 19.8834806136117 23.6355150917009 +T1AvsT1K_api-mir-981 T1AvsT1K api-mir-981 0.407076630077546 1.32599618993863 0.538448138572079 T1A=T1K 0 0.682814668479086 15.6864006352302 15.4284020425891 +T1AvsT1K_api-mir-8 T1AvsT1K api-mir-8 0.1376371586873 1.10010189626725 0.563380782843039 T1A=T1K 0 0.709292352500229 6852.54595327988 6234.11314807414 +T1AvsT1K_api-mir-92b-1 T1AvsT1K api-mir-92b-1 0.130695773754039 1.09482157752109 0.604474367738101 T1A=T1K 0 0.7502341443558 387.715661705752 354.519703647672 +T1AvsT1K_api-mir-92b-2 T1AvsT1K api-mir-92b-2 0.130695773754039 1.09482157752109 0.604474367738101 T1A=T1K 0 0.7502341443558 387.715661705752 354.519703647672 +T1AvsT1K_GL349714_13724 T1AvsT1K GL349714_13724 0.245777798982029 1.1857318612859 0.64316360023848 T1A=T1K 0 0.755393490212979 141.498061593658 121.364759158602 +T1AvsT1K_GL349714_13726 T1AvsT1K GL349714_13726 0.245777798982029 1.1857318612859 0.64316360023848 T1A=T1K 0 0.755393490212979 141.498061593658 121.364759158602 +T1AvsT1K_GL349714_13728 T1AvsT1K GL349714_13728 0.245777798982029 1.1857318612859 0.64316360023848 T1A=T1K 0 0.755393490212979 141.498061593658 121.364759158602 +T1AvsT1K_api-mir-263a T1AvsT1K api-mir-263a 0.275578066976019 1.21047901344396 0.631060987272467 T1A=T1K 0 0.755393490212979 114738.540121811 94800.7276519968 +T1AvsT1K_api-mir-263b T1AvsT1K api-mir-263b 0.34807841767474 1.27286411991236 0.617461696981064 T1A=T1K 0 0.755393490212979 1251.71642775122 994.460582209598 +T1AvsT1K_api-mir-3027 T1AvsT1K api-mir-3027 0.176613068481295 1.13022739892785 0.619137194777729 T1A=T1K 0 0.755393490212979 404.312998546403 362.527824297402 +T1AvsT1K_api-mir-3032 T1AvsT1K api-mir-3032 -0.233803916718824 1.17593141321262 0.631231406004784 T1A=T1K 0 0.755393490212979 31.6881532348652 36.4674445149938 +T1AvsT1K_api-mir-971 T1AvsT1K api-mir-971 -0.450938205848111 1.36692890178478 0.640543437571988 T1A=T1K 0 0.755393490212979 10.1407187013823 19.7487913349406 +T1AvsT1K_api-mir-29 T1AvsT1K api-mir-29 0.170042832942068 1.12509188764571 0.649297373393611 T1A=T1K 0 0.757513602292546 105.245364266731 94.6171458451392 +T1AvsT1K_GL350223_34252 T1AvsT1K GL350223_34252 -0.390391727934582 1.31074925688528 0.706305457833014 T1A=T1K 0 0.808240019658039 21.0291469282923 33.5756424868145 +T1AvsT1K_api-mir-137 T1AvsT1K api-mir-137 0.186715835542089 1.13816982419691 0.706632702901028 T1A=T1K 0 0.808240019658039 31.1024416700597 30.2080451857782 +T1AvsT1K_api-mir-317 T1AvsT1K api-mir-317 0.154683152724126 1.11317711342353 0.70119192803689 T1A=T1K 0 0.808240019658039 41.9865638867419 39.973195910454 +T1AvsT1K_api-mir-1 T1AvsT1K api-mir-1 0.206633192721761 1.15399197610351 0.715386664916463 T1A=T1K 0 0.812939391950526 180.619849632683 163.746504291107 +T1AvsT1K_GL350343_36481 T1AvsT1K GL350343_36481 0.135258154903011 1.09828932337501 0.753231343222206 T1A=T1K 0 0.844971058101834 21.1875817224896 18.2147172220669 +T1AvsT1K_api-mir-190 T1AvsT1K api-mir-190 0.107095457169907 1.07705763828919 0.750699383766064 T1A=T1K 0 0.844971058101834 234.550188295047 221.766347279128 +T1AvsT1K_api-mir-3031 T1AvsT1K api-mir-3031 -0.127017586898592 1.09203385789487 0.759337885524585 T1A=T1K 0 0.846395732272626 167.696215387838 188.245374819867 +T1AvsT1K_api-let-7 T1AvsT1K api-let-7 -0.154131118343296 1.11275124761865 0.777366978733461 T1A=T1K 0 0.861007729609846 17.1052875628726 20.3697975474495 +T1AvsT1K_api-mir-3036-1 T1AvsT1K api-mir-3036-1 -0.0717554902779335 1.05099477011198 0.820621713010342 T1A=T1K 0 0.884509709914779 355.864419414785 378.098568231729 +T1AvsT1K_api-mir-3036-2 T1AvsT1K api-mir-3036-2 -0.0717554902779335 1.05099477011198 0.820621713010342 T1A=T1K 0 0.884509709914779 355.864419414785 378.098568231729 +T1AvsT1K_api-mir-3036-3 T1AvsT1K api-mir-3036-3 -0.0704524082070421 1.05004591114379 0.823857615520622 T1A=T1K 0 0.884509709914779 356.02291302258 377.932084361907 +T1AvsT1K_api-mir-3036-4 T1AvsT1K api-mir-3036-4 -0.0704524082070421 1.05004591114379 0.823857615520622 T1A=T1K 0 0.884509709914779 356.02291302258 377.932084361907 +T1AvsT1K_api-mir-3036-5 T1AvsT1K api-mir-3036-5 -0.0704524082070421 1.05004591114379 0.823857615520622 T1A=T1K 0 0.884509709914779 356.02291302258 377.932084361907 +T1AvsT1K_GL350343_36473 T1AvsT1K GL350343_36473 -0.0803215727804929 1.05725367325285 0.843102219890161 T1A=T1K 0 0.894199324125928 162.229342389252 175.96217279623 +T1AvsT1K_api-mir-9a T1AvsT1K api-mir-9a 0.0552772681366053 1.03905877835059 0.841852631382137 T1A=T1K 0 0.894199324125928 812.438450656032 786.952021519981 +T1AvsT1K_GL350222_34242 T1AvsT1K GL350222_34242 0.0435103136018807 1.0306184420166 0.865141422507651 T1A=T1K 0 0.912046680354452 207.385266113065 204.094293618538 +T1AvsT1K_api-mir-278 T1AvsT1K api-mir-278 0.0916778374889447 1.06560875263065 0.871969642453005 T1A=T1K 0 0.913740643289077 41.6572236507995 44.3288514195503 +T1AvsT1K_api-mir-13a T1AvsT1K api-mir-13a -0.0577710158969872 1.04085638017562 0.880278617656449 T1A=T1K 0 0.916956893392134 2096.25066535355 2190.65508578226 +T1AvsT1K_api-mir-100 T1AvsT1K api-mir-100 0.0779682997371763 1.05553052426604 0.909634934101297 T1A=T1K 0 0.941929665489509 36.6867961405426 37.0363811562773 +T1AvsT1K_api-mir-1000 T1AvsT1K api-mir-1000 0.0256716372214375 1.01795348338184 0.941634856429541 T1A=T1K 0 0.952967111416255 53.3343119331074 54.472321032134 +T1AvsT1K_api-mir-2765 T1AvsT1K api-mir-2765 0.017272797414015 1.0120445491827 0.945284347259186 T1A=T1K 0 0.952967111416255 504.166562590324 501.98589724328 +T1AvsT1K_api-mir-3024 T1AvsT1K api-mir-3024 0.0424576452626954 1.02986672133513 0.927125295801725 T1A=T1K 0 0.952967111416255 32.9381588675413 31.2093737502546 +T1AvsT1K_api-mir-3047-1 T1AvsT1K api-mir-3047-1 0.0434904464155084 1.03060424958709 0.947521585065305 T1A=T1K 0 0.952967111416255 203.230252972802 205.085416847614 +T1AvsT1K_api-mir-3047-2 T1AvsT1K api-mir-3047-2 0.0434904464155084 1.03060424958709 0.947521585065305 T1A=T1K 0 0.952967111416255 203.230252972802 205.085416847614 +T1AvsT1K_api-mir-7 T1AvsT1K api-mir-7 -0.0166613391579242 1.01161570465349 0.969415185409705 T1A=T1K 0 0.969415185409705 181.345502480794 189.343819213867
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AskoT1vsT0.txt Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,176 @@ +Test_id measured_in@Contrast is@gene logFC FC PValue Expression Significance FDR T1/T1A T1/T1K T0/T0A +T1vsT0_api-mir-929 T1vsT0 api-mir-929 1.52200528879093 2.87189954935435 0.000170167334348828 T1>T0 1 0.0297792835110449 45.7383427423633 30.9159434838904 13.4370060260247 +T1vsT0_api-mir-92b-1 T1vsT0 api-mir-92b-1 -0.80417146137229 1.74614269544508 0.00072380827948343 T1<T0 -1 0.0422221496365334 387.715661705752 354.519703647672 646.587652568849 +T1vsT0_api-mir-92b-2 T1vsT0 api-mir-92b-2 -0.80417146137229 1.74614269544508 0.00072380827948343 T1<T0 -1 0.0422221496365334 387.715661705752 354.519703647672 646.587652568849 +T1vsT0_api-let-7 T1vsT0 api-let-7 -1.53453421279761 2.89694885184873 0.00146821012161706 T1=T0 0 0.0642341928207463 17.1052875628726 20.3697975474495 51.7676372940973 +T1vsT0_api-mir-927 T1vsT0 api-mir-927 1.15503837103483 2.22690246409265 0.00200001763952061 T1=T0 0 0.0700006173832214 1222.6871883341 742.960038441659 427.238639370503 +T1vsT0_api-mir-3049 T1vsT0 api-mir-3049 1.17606609803573 2.2595979517563 0.00334451529015501 T1=T0 0 0.0975483626295212 94.7105661640103 53.1156765046011 30.8771272639274 +T1vsT0_api-mir-1000 T1vsT0 api-mir-1000 0.928576960535918 1.90339760451986 0.00667764422859585 T1=T0 0 0.129843082222697 53.3343119331074 54.472321032134 28.0436223189252 +T1vsT0_api-mir-2c T1vsT0 api-mir-2c -0.678556842418134 1.60053790308009 0.00563721477548487 T1=T0 0 0.129843082222697 49.1092218181985 66.1195303451075 90.5431058071145 +T1vsT0_api-mir-3032 T1vsT0 api-mir-3032 -1.17166162670415 2.25271003879347 0.00666595628195355 T1=T0 0 0.129843082222697 31.6881532348652 36.4674445149938 77.401034703635 +T1vsT0_api-mir-92a-1 T1vsT0 api-mir-92a-1 -0.788487446647344 1.72726261270839 0.00912051552886509 T1=T0 0 0.14509911068649 72.386227867033 54.1490720179198 108.083086611924 +T1vsT0_api-mir-92a-2 T1vsT0 api-mir-92a-2 -0.788487446647344 1.72726261270839 0.00912051552886509 T1=T0 0 0.14509911068649 72.386227867033 54.1490720179198 108.083086611924 +T1vsT0_GL350757_41318 T1vsT0 GL350757_41318 0.667804971676578 1.58865402613014 0.0177413336544925 T1=T0 0 0.163407020501905 154.093033384431 133.130797853428 88.834921709588 +T1vsT0_GL350757_41320 T1vsT0 GL350757_41320 0.667804971676578 1.58865402613014 0.0177413336544925 T1=T0 0 0.163407020501905 154.093033384431 133.130797853428 88.834921709588 +T1vsT0_GL350757_41322 T1vsT0 GL350757_41322 0.667804971676578 1.58865402613014 0.0177413336544925 T1=T0 0 0.163407020501905 154.093033384431 133.130797853428 88.834921709588 +T1vsT0_GL350757_41324 T1vsT0 GL350757_41324 0.667804971676578 1.58865402613014 0.0177413336544925 T1=T0 0 0.163407020501905 154.093033384431 133.130797853428 88.834921709588 +T1vsT0_GL350757_41326 T1vsT0 GL350757_41326 0.667804971676578 1.58865402613014 0.0177413336544925 T1=T0 0 0.163407020501905 154.093033384431 133.130797853428 88.834921709588 +T1vsT0_GL350757_41328 T1vsT0 GL350757_41328 0.667804971676578 1.58865402613014 0.0177413336544925 T1=T0 0 0.163407020501905 154.093033384431 133.130797853428 88.834921709588 +T1vsT0_api-mir-3024 T1vsT0 api-mir-3024 -1.02252339864184 2.03146906938746 0.0118617416669047 T1=T0 0 0.163407020501905 32.9381588675413 31.2093737502546 64.7212050546698 +T1vsT0_api-mir-87a T1vsT0 api-mir-87a 0.670153407973832 1.59124216214274 0.0147127885334211 T1=T0 0 0.163407020501905 359.274465229513 241.568668415364 183.898246585246 +T1vsT0_GL349826_21746 T1vsT0 GL349826_21746 0.855235891010956 1.80905452436164 0.019806064601511 T1=T0 0 0.170889771265973 36.9544600878111 24.0458636715105 16.4951684939482 +T1vsT0_api-mir-315 T1vsT0 api-mir-315 -0.500904121575693 1.41510011267714 0.0205067725519167 T1=T0 0 0.170889771265973 20928.2550507448 16149.5398678988 26012.4718189252 +T1vsT0_api-mir-279a T1vsT0 api-mir-279a -0.391706524343188 1.31194434933307 0.025491145454786 T1=T0 0 0.202770475208525 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0.345362058852897 18.2112883523139 38.1421525702081 48.45059536847 +T1vsT0_api-mir-3055-4 T1vsT0 api-mir-3055-4 -0.828017877474729 1.77524467273975 0.16524976325067 T1=T0 0 0.345362058852897 18.2112883523139 38.1421525702081 48.45059536847 +T1vsT0_api-mir-3055-5 T1vsT0 api-mir-3055-5 -0.828017877474729 1.77524467273975 0.16524976325067 T1=T0 0 0.345362058852897 18.2112883523139 38.1421525702081 48.45059536847 +T1vsT0_api-mir-8 T1vsT0 api-mir-8 0.301387655866288 1.23232915897502 0.155668223825451 T1=T0 0 0.345362058852897 6852.54595327988 6234.11314807414 5301.5246677413 +T1vsT0_api-mir-998 T1vsT0 api-mir-998 -0.270355221849614 1.2061047594822 0.155333456822636 T1=T0 0 0.345362058852897 35311.3030595825 28527.9229897474 38278.9942265222 +T1vsT0_GL350151_32890 T1vsT0 GL350151_32890 -0.624783371233295 1.54197927117204 0.210121605438243 T1=T0 0 0.38303417658013 17.5104113748143 42.2838873109649 42.7373848463161 +T1vsT0_api-mir-3027 T1vsT0 api-mir-3027 -0.374004072972836 1.29594462409968 0.221569133569384 T1=T0 0 0.399738127573631 404.312998546403 362.527824297402 492.94034451663 +T1vsT0_GL349919_26520 T1vsT0 GL349919_26520 -0.444615031913279 1.36095091252225 0.224044783872919 T1=T0 0 0.40007997120164 72.073883410293 116.176752645774 124.499541153818 +T1vsT0_GL349642_4949 T1vsT0 GL349642_4949 -0.883992175219735 1.84547497593283 0.248222658737491 T1=T0 0 0.4341360854419 6.08975436654529 16.9645086841215 20.0252950737267 +T1vsT0_GL349643_5182 T1vsT0 GL349643_5182 -0.791972149638995 1.7314397063134 0.262629842463207 T1=T0 0 0.4341360854419 4.31590876285712 16.8703162971331 15.5109406348709 +T1vsT0_GL349919_26542 T1vsT0 GL349919_26542 -0.880545815490303 1.84107170302585 0.262962428896236 T1=T0 0 0.4341360854419 24.4503049468148 89.0011005229108 88.0847020607618 +T1vsT0_GL349919_26564 T1vsT0 GL349919_26564 -0.880545815490303 1.84107170302585 0.262962428896236 T1=T0 0 0.4341360854419 24.4503049468148 89.0011005229108 88.0847020607618 +T1vsT0_GL349919_26580 T1vsT0 GL349919_26580 -0.878541997888134 1.83851633897005 0.259467467557085 T1=T0 0 0.4341360854419 24.4503049468148 88.2849331910451 87.6254945536924 +T1vsT0_GL349919_26590 T1vsT0 GL349919_26590 -0.880545815490303 1.84107170302585 0.262962428896236 T1=T0 0 0.4341360854419 24.4503049468148 89.0011005229108 88.0847020607618 +T1vsT0_GL350151_32872 T1vsT0 GL350151_32872 -0.677355765091056 1.59920597239121 0.253692064784858 T1=T0 0 0.4341360854419 17.422074847417 40.2506014278924 42.6696579688218 +T1vsT0_GL366836_47443 T1vsT0 GL366836_47443 -0.883992175219735 1.84547497593283 0.248222658737491 T1=T0 0 0.4341360854419 6.08975436654529 16.9645086841215 20.0252950737267 +T1vsT0_api-mir-252a T1vsT0 api-mir-252a 0.279069348020315 1.21341188559627 0.276985916154431 T1=T0 0 0.453014348850705 489.114196700038 289.171809924299 308.466786767609 +T1vsT0_api-mir-993 T1vsT0 api-mir-993 0.231078213114539 1.17371180722932 0.291899793963046 T1=T0 0 0.472985777254936 517.095986431029 355.927103464731 364.184068355389 +T1vsT0_GL349714_13724 T1vsT0 GL349714_13724 0.459311564684204 1.37488558405437 0.328835399173946 T1=T0 0 0.512456531236149 141.498061593658 121.364759158602 95.0933122960213 +T1vsT0_GL349714_13726 T1vsT0 GL349714_13726 0.459311564684204 1.37488558405437 0.328835399173946 T1=T0 0 0.512456531236149 141.498061593658 121.364759158602 95.0933122960213 +T1vsT0_GL349714_13728 T1vsT0 GL349714_13728 0.459311564684204 1.37488558405437 0.328835399173946 T1=T0 0 0.512456531236149 141.498061593658 121.364759158602 95.0933122960213 +T1vsT0_GL350677_40695 T1vsT0 GL350677_40695 -0.678753365821881 1.60075594263251 0.327983243298273 T1=T0 0 0.512456531236149 5.6136940181826 13.8990465055077 15.6623504934394 +T1vsT0_GL351656_44870 T1vsT0 GL351656_44870 -0.720371992461227 1.64760680781334 0.33090050302677 T1=T0 0 0.512456531236149 28.7778527542278 98.2409625950879 89.0228336648316 +T1vsT0_GL349645_5442 T1vsT0 GL349645_5442 -0.635051370254868 1.5529930466698 0.354050375382921 T1=T0 0 0.538772310365314 14.8582519250457 52.996163581116 44.1680656848992 +T1vsT0_api-mir-1 T1vsT0 api-mir-1 0.462597587715488 1.37802072674669 0.353357870688933 T1=T0 0 0.538772310365314 180.619849632683 163.746504291107 121.181311601949 +T1vsT0_GL349642_4969 T1vsT0 GL349642_4969 -0.754581305006092 1.68714188351705 0.36989652032334 T1=T0 0 0.543965471063735 6.55800972940896 16.178928282704 18.17295099915 +T1vsT0_GL366836_47439 T1vsT0 GL366836_47439 -0.754581305006092 1.68714188351705 0.36989652032334 T1=T0 0 0.543965471063735 6.55800972940896 16.178928282704 18.17295099915 +T1vsT0_GL366836_47441 T1vsT0 GL366836_47441 -0.754581305006092 1.68714188351705 0.36989652032334 T1=T0 0 0.543965471063735 6.55800972940896 16.178928282704 18.17295099915 +T1vsT0_GL366836_47445 T1vsT0 GL366836_47445 -0.754581305006092 1.68714188351705 0.36989652032334 T1=T0 0 0.543965471063735 6.55800972940896 16.178928282704 18.17295099915 +T1vsT0_GL349645_5438 T1vsT0 GL349645_5438 -0.580401104597611 1.49526491116068 0.409268674845487 T1=T0 0 0.577596920144841 14.9720786249046 42.2540174631687 38.564470100365 +T1vsT0_GL349645_5440 T1vsT0 GL349645_5440 -0.580401104597611 1.49526491116068 0.409268674845487 T1=T0 0 0.577596920144841 14.9720786249046 42.2540174631687 38.564470100365 +T1vsT0_GL349645_5448 T1vsT0 GL349645_5448 -0.58055411835564 1.49542350894499 0.409076368908424 T1=T0 0 0.577596920144841 20.234881500788 66.9746615631992 55.9205425498732 +T1vsT0_GL349645_5452 T1vsT0 GL349645_5452 -0.580401104597611 1.49526491116068 0.409268674845487 T1=T0 0 0.577596920144841 14.9720786249046 42.2540174631687 38.564470100365 +T1vsT0_GL349645_5454 T1vsT0 GL349645_5454 -0.58055411835564 1.49542350894499 0.409076368908424 T1=T0 0 0.577596920144841 20.234881500788 66.9746615631992 55.9205425498732 +T1vsT0_GL349773_18697 T1vsT0 GL349773_18697 -0.386658553876426 1.30736189541788 0.444203121229423 T1=T0 0 0.613383459458722 13.3933664191246 23.7616433874445 24.1677107608458 +T1vsT0_api-mir-137 T1vsT0 api-mir-137 0.326956596512039 1.25436446639169 0.448646187489808 T1=T0 0 0.613383459458722 31.1024416700597 30.2080451857782 23.3256938026282 +T1vsT0_api-mir-275 T1vsT0 api-mir-275 0.288535774589896 1.22140002056932 0.43979952822743 T1=T0 0 0.613383459458722 53.5416861018258 80.9148205341786 52.2616666690044 +T1vsT0_api-mir-971 T1vsT0 api-mir-971 0.629668207441511 1.54720912380252 0.446002819883392 T1=T0 0 0.613383459458722 10.1407187013823 19.7487913349406 7.66479456863866 +T1vsT0_api-mir-184a T1vsT0 api-mir-184a -0.188918345017741 1.13990875326245 0.458262730930718 T1=T0 0 0.621674247386633 48955.440785817 35866.6670300699 47761.3653273075 +T1vsT0_GL350151_32870 T1vsT0 GL350151_32870 -0.537167849718544 1.45112102804964 0.472642602639854 T1=T0 0 0.636249657399803 6.52577459753034 20.259888596177 16.8331341845551 +T1vsT0_api-mir-34 T1vsT0 api-mir-34 -0.206027023104709 1.15350721118837 0.482779995567359 T1=T0 0 0.64493510858235 33.6733146899426 26.767434430309 33.78320785053 +T1vsT0_GL349872_24254 T1vsT0 GL349872_24254 0.137060074120019 1.09966193851187 0.487263425534449 T1=T0 0 0.645993177791883 732.301073986264 610.570405139264 607.144425415593 +T1vsT0_api-mir-306 T1vsT0 api-mir-306 -0.116411554251665 1.08403516292511 0.501007426865275 T1=T0 0 0.65922029850694 1764.58022199887 1478.63566622894 1749.8598153719 +T1vsT0_GL350222_34242 T1vsT0 GL350222_34242 0.148754966629635 1.108612336248 0.504928700150955 T1=T0 0 0.659421809898636 207.385266113065 204.094293618538 184.233673314165 +T1vsT0_GL350682_40710 T1vsT0 GL350682_40710 0.718850155640996 1.64586973474446 0.5245343732306 T1=T0 0 0.677189796763751 11.8785246839619 57.6693961245775 15.1093792744665 +T1vsT0_api-mir-184b T1vsT0 api-mir-184b -0.16639334626544 1.12224941659616 0.526273213484972 T1=T0 0 0.677189796763751 43427.1191642789 32911.4007978194 42422.936024093 +T1vsT0_api-mir-71 T1vsT0 api-mir-71 -0.17873920191839 1.13189426944141 0.553854266442803 T1=T0 0 0.707478077572923 110.914522043777 77.5719375098147 104.833522367662 +T1vsT0_GL350343_36473 T1vsT0 GL350343_36473 -0.19875898563541 1.1477106631003 0.567198973867199 T1=T0 0 0.714099427530646 162.229342389252 175.96217279623 192.03628664115 +T1vsT0_api-mir-316 T1vsT0 api-mir-316 0.237857877547622 1.17924041746979 0.563653082769071 T1=T0 0 0.714099427530646 29.2940452013454 14.9534399843751 18.1123394158094 +T1vsT0_api-mir-279b T1vsT0 api-mir-279b -0.102058637993565 1.07330390968664 0.57995095190047 T1=T0 0 0.724938689875587 615.057540608426 554.283861464607 626.144650512871 +T1vsT0_api-mir-263a T1vsT0 api-mir-263a 0.257329698147274 1.19526432661657 0.608176743975592 T1=T0 0 0.754829292168288 114738.540121811 94800.7276519968 87248.5987485016 +T1vsT0_api-bantam T1vsT0 api-bantam 0.097058232011608 1.06959025926495 0.617038865518444 T1=T0 0 0.760435221589632 16321.2717378554 12158.7515688539 13169.3308517045 +T1vsT0_api-mir-3031 T1vsT0 api-mir-3031 -0.169201827935527 1.12443621742729 0.63332858628247 T1=T0 0 0.769670156940502 167.696215387838 188.245374819867 197.60145077256 +T1vsT0_api-mir-996 T1vsT0 api-mir-996 0.239725716710288 1.1807681539953 0.631241874685807 T1=T0 0 0.769670156940502 30.9540188931113 16.9072732178458 19.6205244782686 +T1vsT0_GL349801_20413 T1vsT0 GL349801_20413 -0.186574723110314 1.1380585033338 0.646580208968097 T1=T0 0 0.780355424616669 19.7476856197604 14.9856656593161 18.9258171290887 +T1vsT0_GL350343_36481 T1vsT0 GL350343_36481 0.165816300611348 1.12180063176152 0.658047580503662 T1=T0 0 0.788755661562608 21.1875817224896 18.2147172220669 18.2496028315714 +T1vsT0_api-mir-3040 T1vsT0 api-mir-3040 0.123383217395928 1.08928631974164 0.682184965900586 T1=T0 0 0.812124959405459 461.832106680395 318.572656659124 353.320213891397 +T1vsT0_api-mir-263b T1vsT0 api-mir-263b -0.230980361370687 1.17363220215058 0.697955834350448 T1=T0 0 0.819746785310929 1251.71642775122 994.460582209598 1300.31895317557 +T1vsT0_api-mir-3018 T1vsT0 api-mir-3018 0.17013415265197 1.12516310596536 0.694541250708202 T1=T0 0 0.819746785310929 25.0073508370315 8.62911781908716 12.9763124689112 +T1vsT0_api-mir-29 T1vsT0 api-mir-29 -0.115561178234384 1.08339638213658 0.718323456811471 T1=T0 0 0.838044032946716 105.245364266731 94.6171458451392 107.910313729097 +T1vsT0_api-mir-9a T1vsT0 api-mir-9a -0.0784502994664945 1.05588323250338 0.742549555556205 T1=T0 0 0.860570676969111 812.438450656032 786.952021519981 841.300362032995 +T1vsT0_api-mir-3050 T1vsT0 api-mir-3050 -0.0803417480204076 1.05726845842578 0.766409541148289 T1=T0 0 0.882379405927306 1142501.70015826 795661.911903157 1008034.59361181 +T1vsT0_api-mir-3033 T1vsT0 api-mir-3033 0.0508557287878096 1.03587916923696 0.789146678837066 T1=T0 0 0.902618750303833 502.552807518651 332.193472624891 394.957854143393 +T1vsT0_api-mir-7 T1vsT0 api-mir-7 -0.0839548640418031 1.05991962237934 0.821089236842164 T1=T0 0 0.933055950957005 181.345502480794 189.343819213867 192.866444597218 +T1vsT0_api-mir-3043-1 T1vsT0 api-mir-3043-1 -0.0606704498728051 1.04295032857273 0.840298758796115 T1=T0 0 0.93663874388102 57.6997552376986 40.4424775820102 50.1296395288814 +T1vsT0_api-mir-3043-2 T1vsT0 api-mir-3043-2 -0.0606704498728051 1.04295032857273 0.840298758796115 T1=T0 0 0.93663874388102 57.6997552376986 40.4424775820102 50.1296395288814 +T1vsT0_api-mir-3043-3 T1vsT0 api-mir-3043-3 -0.0606704498728051 1.04295032857273 0.840298758796115 T1=T0 0 0.93663874388102 57.6997552376986 40.4424775820102 50.1296395288814 +T1vsT0_api-mir-317 T1vsT0 api-mir-317 0.0627695821790897 1.04446893379184 0.855892214174629 T1=T0 0 0.947981882788355 41.9865638867419 39.973195910454 38.1499577028816 +T1vsT0_api-mir-277 T1vsT0 api-mir-277 0.037580817237381 1.02639127891326 0.878902194393551 T1=T0 0 0.967345182508625 95.8454418109413 59.950707904155 74.0187227137694 +T1vsT0_GL349650_6636 T1vsT0 GL349650_6636 0.0164233199330276 1.01144881967945 0.950944499891273 T1=T0 0 0.967532037824197 687.359529366427 484.997109051297 571.761575450836 +T1vsT0_GL349650_6638 T1vsT0 GL349650_6638 0.0164233199330276 1.01144881967945 0.950944499891273 T1=T0 0 0.967532037824197 687.359529366427 484.997109051297 571.761575450836 +T1vsT0_GL349650_6640 T1vsT0 GL349650_6640 0.0164233199330276 1.01144881967945 0.950944499891273 T1=T0 0 0.967532037824197 687.359529366427 484.997109051297 571.761575450836 +T1vsT0_GL349650_6646 T1vsT0 GL349650_6646 0.0164233199330276 1.01144881967945 0.950944499891273 T1=T0 0 0.967532037824197 687.359529366427 484.997109051297 571.761575450836 +T1vsT0_GL349742_15837 T1vsT0 GL349742_15837 -0.0271288863461452 1.01898222557699 0.886388345249162 T1=T0 0 0.967532037824197 16838.4837907878 12660.4383260529 14878.3230778168 +T1vsT0_GL350137_32551 T1vsT0 GL350137_32551 -0.0750197975296233 1.05337549090811 0.933710532905093 T1=T0 0 0.967532037824197 204.143997030395 578.995678143302 358.835578453794 +T1vsT0_GL350137_32552 T1vsT0 GL350137_32552 -0.0737373050949295 1.05243950251709 0.935206728203719 T1=T0 0 0.967532037824197 116.544493511701 279.125976791414 186.851752515656 +T1vsT0_GL355572_46131 T1vsT0 GL355572_46131 0.0164233356871345 1.01144883072439 0.950945774318639 T1=T0 0 0.967532037824197 687.359529366427 484.997109051297 571.761575450836 +T1vsT0_api-mir-10 T1vsT0 api-mir-10 0.0311495747947241 1.02182601743353 0.937687018813089 T1=T0 0 0.967532037824197 1609762.52422668 1080955.87403039 1290939.44087786 +T1vsT0_api-mir-190 T1vsT0 api-mir-190 -0.0356914356001437 1.02504797662293 0.901881664477287 T1=T0 0 0.967532037824197 234.550188295047 221.766347279128 231.485466971721 +T1vsT0_api-mir-278 T1vsT0 api-mir-278 -0.0362475819316304 1.02544319983334 0.939540537737326 T1=T0 0 0.967532037824197 41.6572236507995 44.3288514195503 41.1737470124825 +T1vsT0_api-mir-3041 T1vsT0 api-mir-3041 0.0411648933341176 1.02894430472213 0.89846959252644 T1=T0 0 0.967532037824197 83.1697934295355 68.7196716946604 73.6148441337726 +T1vsT0_api-mir-9b T1vsT0 api-mir-9b 0.0164413646692999 1.01146147061456 0.942020116365711 T1=T0 0 0.967532037824197 436.573003510837 335.799016629453 376.361439667079 +T1vsT0_api-mir-252b T1vsT0 api-mir-252b 0.0211214044961437 1.01474793522848 0.961180689316308 T1=T0 0 0.972292604799733 80.5998452829956 66.0945308776993 70.3219832837863 +T1vsT0_GL350223_34252 T1vsT0 GL350223_34252 -0.0338080435006178 1.02371068245646 0.967881073478121 T1=T0 0 0.973443608383168 21.0291469282923 33.5756424868145 24.5027562953933 +T1vsT0_GL350370_36909 T1vsT0 GL350370_36909 0.00621519395425303 1.00431733712833 0.981568484688693 T1=T0 0 0.981568484688693 656.82657433825 458.154802585589 547.199142865752
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AskoT1vsT2.txt Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,176 @@ +Test_id measured_in@Contrast is@gene logFC FC PValue Expression Significance FDR T1/T1A T1/T1K T2/T2A T2/T2K +T1vsT2_api-mir-3024 T1vsT2 api-mir-3024 3.12174170464632 8.70438099023781 9.00393166340146e-05 T1>T2 1 0.0157568804109526 32.9381588675413 31.2093737502546 9.39844720626758 12.6426867572395 +T1vsT2_api-mir-316 T1vsT2 api-mir-316 -2.56031506201473 5.89836483907807 0.000564267422216593 T1<T2 -1 0.0493733994439519 29.2940452013454 14.9534399843751 47.3316760732136 57.1450820793195 +T1vsT2_GL350757_41318 T1vsT2 GL350757_41318 -1.2236513594056 2.33537035719147 0.0070903245043704 T1=T2 0 0.0689337104591566 154.093033384431 133.130797853428 222.856316018568 210.398577789772 +T1vsT2_GL350757_41320 T1vsT2 GL350757_41320 -1.2236513594056 2.33537035719147 0.0070903245043704 T1=T2 0 0.0689337104591566 154.093033384431 133.130797853428 222.856316018568 210.398577789772 +T1vsT2_GL350757_41322 T1vsT2 GL350757_41322 -1.2236513594056 2.33537035719147 0.0070903245043704 T1=T2 0 0.0689337104591566 154.093033384431 133.130797853428 222.856316018568 210.398577789772 +T1vsT2_GL350757_41324 T1vsT2 GL350757_41324 -1.2236513594056 2.33537035719147 0.0070903245043704 T1=T2 0 0.0689337104591566 154.093033384431 133.130797853428 222.856316018568 210.398577789772 +T1vsT2_GL350757_41326 T1vsT2 GL350757_41326 -1.2236513594056 2.33537035719147 0.0070903245043704 T1=T2 0 0.0689337104591566 154.093033384431 133.130797853428 222.856316018568 210.398577789772 +T1vsT2_GL350757_41328 T1vsT2 GL350757_41328 -1.2236513594056 2.33537035719147 0.0070903245043704 T1=T2 0 0.0689337104591566 154.093033384431 133.130797853428 222.856316018568 210.398577789772 +T1vsT2_api-mir-1 T1vsT2 api-mir-1 -2.32668513849045 5.01651386769124 0.00690315235901703 T1=T2 0 0.0689337104591566 180.619849632683 163.746504291107 381.774966277306 371.099133673289 +T1vsT2_api-mir-14 T1vsT2 api-mir-14 -1.75201918397251 3.36829660344174 0.00135175295890012 T1=T2 0 0.0689337104591566 5174.26337501864 4324.71028742041 9057.45291271703 8316.36967033474 +T1vsT2_api-mir-210 T1vsT2 api-mir-210 -1.99423211838173 3.98403996177628 0.00219873520800795 T1=T2 0 0.0689337104591566 45.7488925668745 20.0195697686999 66.6050846850626 60.1807998129075 +T1vsT2_api-mir-3016 T1vsT2 api-mir-3016 2.8083270926824 7.00471859094321 0.0027257406187562 T1=T2 0 0.0689337104591566 10.4497505123629 21.1433464017102 5.33918096274054 5.2451550522054 +T1vsT2_api-mir-3018 T1vsT2 api-mir-3018 -2.08253865932694 4.23551870074831 0.00531939401449926 T1=T2 0 0.0689337104591566 25.0073508370315 8.62911781908716 30.3840920325039 31.7226039874993 +T1vsT2_api-mir-929 T1vsT2 api-mir-929 -1.64972083151462 3.13772916703121 0.00343047066299578 T1=T2 0 0.0689337104591566 45.7383427423633 30.9159434838904 73.3466164710049 60.643677777599 +T1vsT2_api-mir-92a-1 T1vsT2 api-mir-92a-1 1.52984952229575 2.88755719389213 0.0035885903084464 T1=T2 0 0.0689337104591566 72.386227867033 54.1490720179198 35.5759781605864 38.8155292844677 +T1vsT2_api-mir-92a-2 T1vsT2 api-mir-92a-2 1.52984952229575 2.88755719389213 0.0035885903084464 T1=T2 0 0.0689337104591566 72.386227867033 54.1490720179198 35.5759781605864 38.8155292844677 +T1vsT2_api-mir-92b-1 T1vsT2 api-mir-92b-1 1.05599824524424 2.07915634146282 0.00607088774431841 T1=T2 0 0.0689337104591566 387.715661705752 354.519703647672 262.91725714257 251.764612041121 +T1vsT2_api-mir-92b-2 T1vsT2 api-mir-92b-2 1.05599824524424 2.07915634146282 0.00607088774431841 T1=T2 0 0.0689337104591566 387.715661705752 354.519703647672 262.91725714257 251.764612041121 +T1vsT2_api-mir-927 T1vsT2 api-mir-927 -1.40356536452645 2.64554574582873 0.0123315109227036 T1=T2 0 0.113579705867007 1222.6871883341 742.960038441659 1720.16476297276 1394.20082468705 +T1vsT2_GL349826_21746 T1vsT2 GL349826_21746 -1.19291272037751 2.28613836070488 0.0341430337873126 T1=T2 0 0.288955230397108 36.9544600878111 24.0458636715105 51.7665621942847 39.7552622980635 +T1vsT2_GL350222_34242 T1vsT2 GL350222_34242 -0.79707086088568 1.73756971245709 0.034674627647653 T1=T2 0 0.288955230397108 207.385266113065 204.094293618538 271.536440873514 267.557984759917 +T1vsT2_api-mir-87b T1vsT2 api-mir-87b -0.966857100334667 1.95457792131246 0.0547115040296977 T1=T2 0 0.435205145690778 178.020931797068 136.169251352098 227.212497056194 204.421850406862 +T1vsT2_GL349650_6636 T1vsT2 GL349650_6636 -0.789610976526501 1.72860827963722 0.0791797712306615 T1=T2 0 0.461881998845525 687.359529366427 484.997109051297 806.208552002674 718.499068558673 +T1vsT2_GL349650_6638 T1vsT2 GL349650_6638 -0.789610976526501 1.72860827963722 0.0791797712306615 T1=T2 0 0.461881998845525 687.359529366427 484.997109051297 806.208552002674 718.499068558673 +T1vsT2_GL349650_6640 T1vsT2 GL349650_6640 -0.789610976526501 1.72860827963722 0.0791797712306615 T1=T2 0 0.461881998845525 687.359529366427 484.997109051297 806.208552002674 718.499068558673 +T1vsT2_GL349650_6646 T1vsT2 GL349650_6646 -0.789610976526501 1.72860827963722 0.0791797712306615 T1=T2 0 0.461881998845525 687.359529366427 484.997109051297 806.208552002674 718.499068558673 +T1vsT2_GL350370_36909 T1vsT2 GL350370_36909 -0.803215163401591 1.74498563912862 0.076560223784824 T1=T2 0 0.461881998845525 656.82657433825 458.154802585589 772.848538093928 683.318052615232 +T1vsT2_GL355572_46131 T1vsT2 GL355572_46131 -0.789935809950406 1.72899753235447 0.0790715830532902 T1=T2 0 0.461881998845525 687.359529366427 484.997109051297 806.389998999727 718.499068558673 +T1vsT2_api-mir-3040 T1vsT2 api-mir-3040 -0.897553308668131 1.8629039716922 0.0755867195975235 T1=T2 0 0.461881998845525 461.832106680395 318.572656659124 577.80634143084 478.13260602389 +T1vsT2_api-mir-981 T1vsT2 api-mir-981 -1.63363717113863 3.10294294804171 0.0772866140703316 T1=T2 0 0.461881998845525 15.6864006352302 15.4284020425891 24.0573219619243 23.8163580683543 +T1vsT2_api-mir-277 T1vsT2 api-mir-277 -0.702485569116227 1.6273060078929 0.0891588697883581 T1=T2 0 0.503316200418151 95.8454418109413 59.950707904155 101.094878069469 93.4734733070941 +T1vsT2_api-mir-2a T1vsT2 api-mir-2a 0.592757800182097 1.50812687091163 0.105441465776607 T1=T2 0 0.57663301596582 1126.12814528614 834.523638972188 804.844874667114 772.441552001314 +T1vsT2_GL350468_38246 T1vsT2 GL350468_38246 -0.797136982784513 1.73764935093813 0.121848210125341 T1=T2 0 0.641206908584688 683.497118292956 521.57331291497 796.136724378387 769.858616409501 +T1vsT2_api-mir-276 T1vsT2 api-mir-276 -0.549875434413753 1.46395928889856 0.124577342239311 T1=T2 0 0.641206908584688 44732.2556555246 36053.6225796423 49739.6581555238 47461.596670029 +T1vsT2_GL349642_4945 T1vsT2 GL349642_4945 0.908203710759888 1.87670736826185 0.337121415867633 T1=T2 0 0.819392330233829 116.896489669693 328.413968129475 101.61231882496 202.836868768343 +T1vsT2_GL349642_4947 T1vsT2 GL349642_4947 1.10590831711736 2.15234346437182 0.321978941028497 T1=T2 0 0.819392330233829 10.8735388983366 23.3733601863652 8.98727321466557 13.5611421639255 +T1vsT2_GL349642_4951 T1vsT2 GL349642_4951 1.10590831711736 2.15234346437182 0.321978941028497 T1=T2 0 0.819392330233829 10.8735388983366 23.3733601863652 8.98727321466557 13.5611421639255 +T1vsT2_GL349642_4955 T1vsT2 GL349642_4955 1.10590831711736 2.15234346437182 0.321978941028497 T1=T2 0 0.819392330233829 10.8735388983366 23.3733601863652 8.98727321466557 13.5611421639255 +T1vsT2_GL349642_4959 T1vsT2 GL349642_4959 0.908203710759888 1.87670736826185 0.337121415867633 T1=T2 0 0.819392330233829 116.896489669693 328.413968129475 101.61231882496 202.836868768343 +T1vsT2_GL349642_4961 T1vsT2 GL349642_4961 0.982717489583993 1.97618428613697 0.298821070762313 T1=T2 0 0.819392330233829 26.2552964125283 69.0764764157016 20.5220334361146 45.5079252688433 +T1vsT2_GL349642_4963 T1vsT2 GL349642_4963 0.908203710759888 1.87670736826185 0.337121415867633 T1=T2 0 0.819392330233829 116.896489669693 328.413968129475 101.61231882496 202.836868768343 +T1vsT2_GL349642_4965 T1vsT2 GL349642_4965 1.10590831711736 2.15234346437182 0.321978941028497 T1=T2 0 0.819392330233829 10.8735388983366 23.3733601863652 8.98727321466557 13.5611421639255 +T1vsT2_GL349643_5182 T1vsT2 GL349643_5182 1.32531382962428 2.50587392101724 0.291846146303744 T1=T2 0 0.819392330233829 4.31590876285712 16.8703162971331 4.05931469749039 7.7464892270617 +T1vsT2_GL349714_13724 T1vsT2 GL349714_13724 0.787992764968093 1.72667045797497 0.297606432357582 T1=T2 0 0.819392330233829 141.498061593658 121.364759158602 106.753742722073 93.184513796073 +T1vsT2_GL349714_13726 T1vsT2 GL349714_13726 0.787992764968093 1.72667045797497 0.297606432357582 T1=T2 0 0.819392330233829 141.498061593658 121.364759158602 106.753742722073 93.184513796073 +T1vsT2_GL349714_13728 T1vsT2 GL349714_13728 0.787992764968093 1.72667045797497 0.297606432357582 T1=T2 0 0.819392330233829 141.498061593658 121.364759158602 106.753742722073 93.184513796073 +T1vsT2_GL350137_32551 T1vsT2 GL350137_32551 1.86136316065593 3.63350819621238 0.219956532410199 T1=T2 0 0.819392330233829 204.143997030395 578.995678143302 103.57230467644 306.013099511433 +T1vsT2_GL350137_32552 T1vsT2 GL350137_32552 2.01263788968201 4.03519359183607 0.189735101364933 T1=T2 0 0.819392330233829 116.544493511701 279.125976791414 51.6643780671411 148.931866740123 +T1vsT2_GL350151_32890 T1vsT2 GL350151_32890 0.87785327157497 1.83763886150669 0.296550385059179 T1=T2 0 0.819392330233829 17.5104113748143 42.2838873109649 16.8987752295306 24.3082253888476 +T1vsT2_GL350151_32910 T1vsT2 GL350151_32910 0.800431979929181 1.7416225350212 0.332990589740301 T1=T2 0 0.819392330233829 17.7366251545205 42.92724866839 17.080222226584 26.2029181411405 +T1vsT2_GL350223_34252 T1vsT2 GL350223_34252 1.87356478232482 3.66436898210636 0.203073217619496 T1=T2 0 0.819392330233829 21.0291469282923 33.5756424868145 5.41058465149451 27.8738652634777 +T1vsT2_GL350343_36481 T1vsT2 GL350343_36481 -0.832202903741258 1.78040184845228 0.17506545868888 T1=T2 0 0.819392330233829 21.1875817224896 18.2147172220669 25.0627364783323 30.1075528576254 +T1vsT2_GL350677_40695 T1vsT2 GL350677_40695 1.20214024996852 2.30080744622618 0.311028596546837 T1=T2 0 0.819392330233829 5.6136940181826 13.8990465055077 2.62846685096616 13.43609533459 +T1vsT2_GL350737_41242 T1vsT2 GL350737_41242 0.800431979929181 1.7416225350212 0.332990589740301 T1=T2 0 0.819392330233829 17.7366251545205 42.92724866839 17.080222226584 26.2029181411405 +T1vsT2_api-bantam T1vsT2 api-bantam -0.363265369174785 1.28633406982524 0.255013896543067 T1=T2 0 0.819392330233829 16321.2717378554 12158.7515688539 17078.3447005196 14944.9044554132 +T1vsT2_api-mir-100 T1vsT2 api-mir-100 0.95547265754544 1.93921485779404 0.327267352378279 T1=T2 0 0.819392330233829 36.6867961405426 37.0363811562773 21.1027075981608 30.2097239192629 +T1vsT2_api-mir-1000 T1vsT2 api-mir-1000 -0.528665955630578 1.44259462706928 0.289390938974423 T1=T2 0 0.819392330233829 53.3343119331074 54.472321032134 69.9973296535426 58.6612204191131 +T1vsT2_api-mir-13a T1vsT2 api-mir-13a 0.586361716231254 1.5014554991315 0.285194940975003 T1=T2 0 0.819392330233829 2096.25066535355 2190.65508578226 1719.53052217228 1773.7552599596 +T1vsT2_api-mir-252a T1vsT2 api-mir-252a -0.442606555616151 1.35905755616482 0.28554521984857 T1=T2 0 0.819392330233829 489.114196700038 289.171809924299 480.543592935641 396.625013068125 +T1vsT2_api-mir-263a T1vsT2 api-mir-263a -0.793266792251924 1.73299415936275 0.332120373749546 T1=T2 0 0.819392330233829 114738.540121811 94800.7276519968 163679.522376229 115147.562359967 +T1vsT2_api-mir-263b T1vsT2 api-mir-263b -1.043423639938 2.0611130535761 0.293248344247114 T1=T2 0 0.819392330233829 1251.71642775122 994.460582209598 1893.61155692519 1337.23450831487 +T1vsT2_api-mir-279a T1vsT2 api-mir-279a 0.310184554206545 1.23986629749359 0.267538825345607 T1=T2 0 0.819392330233829 1807.69888237487 1417.07904547563 1441.70044089313 1432.98876412673 +T1vsT2_api-mir-2b T1vsT2 api-mir-2b 0.514406996426605 1.42840688846883 0.175524558288475 T1=T2 0 0.819392330233829 532.896316982273 446.401152061298 425.755249577495 389.33468630738 +T1vsT2_api-mir-3049 T1vsT2 api-mir-3049 -0.706205485668349 1.63150734867717 0.216969506883755 T1=T2 0 0.819392330233829 94.7105661640103 53.1156765046011 109.554845586267 72.0853763631651 +T1vsT2_api-mir-306 T1vsT2 api-mir-306 0.357491451637538 1.28119622433988 0.212976884669674 T1=T2 0 0.819392330233829 1764.58022199887 1478.63566622894 1475.95237679632 1378.31249240608 +T1vsT2_api-mir-315 T1vsT2 api-mir-315 0.398650184859462 1.31827392940308 0.24782133714804 T1=T2 0 0.819392330233829 20928.2550507448 16149.5398678988 16207.8874348461 15815.8285621859 +T1vsT2_api-mir-34 T1vsT2 api-mir-34 -0.671334912956692 1.59254585456881 0.171233404747116 T1=T2 0 0.819392330233829 33.6733146899426 26.767434430309 36.5841102943991 37.427678364582 +T1vsT2_api-mir-71 T1vsT2 api-mir-71 0.62006401316559 1.53694337479066 0.219646068919577 T1=T2 0 0.819392330233829 110.914522043777 77.5719375098147 80.0860394443051 70.4597414922617 +T1vsT2_api-mir-8 T1vsT2 api-mir-8 -0.382586155887927 1.30367671558932 0.260435156342527 T1=T2 0 0.819392330233829 6852.54595327988 6234.11314807414 7719.78126352141 7208.95715011336 +T1vsT2_api-mir-87a T1vsT2 api-mir-87a -0.515553265184968 1.42954225580284 0.215641414730815 T1=T2 0 0.819392330233829 359.274465229513 241.568668415364 364.170268143297 336.035634591802 +T1vsT2_api-mir-996 T1vsT2 api-mir-996 0.823854749319571 1.77012930339275 0.313780429942788 T1=T2 0 0.819392330233829 30.9540188931113 16.9072732178458 18.3716222128667 16.5090926445355 +T1vsT2_api-mir-998 T1vsT2 api-mir-998 0.38487084527789 1.3057428875336 0.217845788305927 T1=T2 0 0.819392330233829 35311.3030595825 28527.9229897474 30986.3919268286 24896.0299871605 +T1vsT2_GL349643_5180 T1vsT2 GL349643_5180 1.14609288840246 2.2131371951755 0.345977828359107 T1=T2 0 0.829398903600599 4.54212254256334 17.4668387068677 4.2586247302231 9.25604252110125 +T1vsT2_api-mir-3032 T1vsT2 api-mir-3032 0.626160727369427 1.54345211796683 0.366291404644829 T1=T2 0 0.866229673146554 31.6881532348652 36.4674445149938 23.4780389246877 32.8486087182833 +T1vsT2_api-mir-10 T1vsT2 api-mir-10 -0.581188231831367 1.49608094284518 0.375270356890806 T1=T2 0 0.875630832745214 1609762.52422668 1080955.87403039 1918869.3641413 1356676.37011057 +T1vsT2_GL349642_4949 T1vsT2 GL349642_4949 0.895067330828115 1.85969667556788 0.495836770638695 T1=T2 0 0.889215137865559 6.08975436654529 16.9645086841215 6.23858283206665 8.91412436283476 +T1vsT2_GL349642_4954 T1vsT2 GL349642_4954 0.862234067745102 1.81785114331854 0.451489906824736 T1=T2 0 0.889215137865559 65.6308127111902 161.027468412219 59.8801426597752 97.8750108681155 +T1vsT2_GL349642_4958 T1vsT2 GL349642_4958 0.862234067745102 1.81785114331854 0.451489906824736 T1=T2 0 0.889215137865559 65.6308127111902 161.027468412219 59.8801426597752 97.8750108681155 +T1vsT2_GL349642_4969 T1vsT2 GL349642_4969 1.11477041285038 2.16560543419223 0.443212933904308 T1=T2 0 0.889215137865559 6.55800972940896 16.178928282704 6.25463860573694 7.5423138852036 +T1vsT2_GL349642_4972 T1vsT2 GL349642_4972 0.862234067745102 1.81785114331854 0.451489906824736 T1=T2 0 0.889215137865559 65.6308127111902 161.027468412219 59.8801426597752 97.8750108681155 +T1vsT2_GL349642_4974 T1vsT2 GL349642_4974 0.774434438456508 1.7105193665773 0.497960477204713 T1=T2 0 0.889215137865559 53.3370100028057 132.896009310663 49.4883060495524 84.7014662816012 +T1vsT2_GL349642_4976 T1vsT2 GL349642_4976 0.862234067745102 1.81785114331854 0.451489906824736 T1=T2 0 0.889215137865559 65.6308127111902 161.027468412219 59.8801426597752 97.8750108681155 +T1vsT2_GL349642_4978 T1vsT2 GL349642_4978 0.850731892713455 1.80341558281948 0.459201642239145 T1=T2 0 0.889215137865559 60.807187993068 150.137655781385 56.6716087462903 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GL366836_47441 1.11477041285038 2.16560543419223 0.443212933904308 T1=T2 0 0.889215137865559 6.55800972940896 16.178928282704 6.25463860573694 7.5423138852036 +T1vsT2_GL366836_47443 T1vsT2 GL366836_47443 0.895067330828115 1.85969667556788 0.495836770638695 T1=T2 0 0.889215137865559 6.08975436654529 16.9645086841215 6.23858283206665 8.91412436283476 +T1vsT2_GL366836_47445 T1vsT2 GL366836_47445 1.11477041285038 2.16560543419223 0.443212933904308 T1=T2 0 0.889215137865559 6.55800972940896 16.178928282704 6.25463860573694 7.5423138852036 +T1vsT2_api-mir-252b T1vsT2 api-mir-252b -0.596605982791365 1.51215495334442 0.402079056594957 T1=T2 0 0.889215137865559 80.5998452829956 66.0945308776993 87.3965220353206 89.0590652091734 +T1vsT2_api-mir-3041 T1vsT2 api-mir-3041 -0.444036826763107 1.36040557817482 0.402179531808058 T1=T2 0 0.889215137865559 83.1697934295355 68.7196716946604 107.017450811661 73.5629952263426 +T1vsT2_api-mir-3055-1 T1vsT2 api-mir-3055-1 0.675953794925866 1.59765266418986 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0.914952463885493 19.8834806136117 23.6355150917009 23.7570879803883 25.688221758373 +T1vsT2_GL349630_2419 T1vsT2 GL349630_2419 0.492603709859455 1.40698184206488 0.646374497790198 T1=T2 0 0.93495837349898 40.7692899051509 112.352482308845 42.5215455530646 77.1738957792082 +T1vsT2_GL349630_2421 T1vsT2 GL349630_2421 0.492603709859455 1.40698184206488 0.646374497790198 T1=T2 0 0.93495837349898 40.7692899051509 112.352482308845 42.5215455530646 77.1738957792082 +T1vsT2_GL349630_2423 T1vsT2 GL349630_2423 0.492603709859455 1.40698184206488 0.646374497790198 T1=T2 0 0.93495837349898 40.7692899051509 112.352482308845 42.5215455530646 77.1738957792082 +T1vsT2_GL349630_2425 T1vsT2 GL349630_2425 0.492603709859455 1.40698184206488 0.646374497790198 T1=T2 0 0.93495837349898 40.7692899051509 112.352482308845 42.5215455530646 77.1738957792082 +T1vsT2_GL349630_2427 T1vsT2 GL349630_2427 0.733418642999605 1.6625741009678 0.660869456323149 T1=T2 0 0.93495837349898 3.31343434155413 13.0513763298296 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T1vsT2 GL349645_5452 0.443982722407377 1.36035456081834 0.70670216942165 T1=T2 0 0.93495837349898 14.9720786249046 42.2540174631687 18.4934008532823 25.5330639918778 +T1vsT2_GL349645_5454 T1vsT2 GL349645_5454 0.581801108885902 1.49671663399409 0.621771766354165 T1=T2 0 0.93495837349898 20.234881500788 66.9746615631992 24.508282544732 37.1908093099749 +T1vsT2_GL349755_17087 T1vsT2 GL349755_17087 0.733418642999605 1.6625741009678 0.660869456323149 T1=T2 0 0.93495837349898 3.31343434155413 13.0513763298296 3.09959689136328 7.70734865102163 +T1vsT2_GL349773_18697 T1vsT2 GL349773_18697 -0.436448265909041 1.3532686455861 0.601546106292998 T1=T2 0 0.93495837349898 13.3933664191246 23.7616433874445 17.0744059570634 27.0937814638994 +T1vsT2_GL349919_26520 T1vsT2 GL349919_26520 0.233284982613031 1.17550850943676 0.697935544520117 T1=T2 0 0.93495837349898 72.073883410293 116.176752645774 70.3745660356144 101.682183109349 +T1vsT2_GL349919_26542 T1vsT2 GL349919_26542 0.405128503772513 1.32420685493208 0.758651937353458 T1=T2 0 0.93495837349898 24.4503049468148 89.0011005229108 31.0941949886553 54.6219198835019 +T1vsT2_GL349919_26564 T1vsT2 GL349919_26564 0.405128503772513 1.32420685493208 0.758651937353458 T1=T2 0 0.93495837349898 24.4503049468148 89.0011005229108 31.0941949886553 54.6219198835019 +T1vsT2_GL349919_26580 T1vsT2 GL349919_26580 0.42115547462011 1.33899954889269 0.747024615600797 T1=T2 0 0.93495837349898 24.4503049468148 88.2849331910451 30.8788291822523 53.9592224886412 +T1vsT2_GL349919_26590 T1vsT2 GL349919_26590 0.405128503772513 1.32420685493208 0.758651937353458 T1=T2 0 0.93495837349898 24.4503049468148 89.0011005229108 31.0941949886553 54.6219198835019 +T1vsT2_GL349928_26838 T1vsT2 GL349928_26838 0.270554451318069 1.20627132843521 0.636099164856198 T1=T2 0 0.93495837349898 48.4496831345842 38.5345853531023 41.0100461864987 35.9090528426243 +T1vsT2_GL350151_32870 T1vsT2 GL350151_32870 0.61480872868589 1.53135495786279 0.632376164769766 T1=T2 0 0.93495837349898 6.52577459753034 20.259888596177 5.93033577721228 15.0244479823509 +T1vsT2_GL350151_32872 T1vsT2 GL350151_32872 0.335455532975869 1.26177575339695 0.735464141259952 T1=T2 0 0.93495837349898 17.422074847417 40.2506014278924 19.9841236092326 27.4418345048662 +T1vsT2_GL350151_32913 T1vsT2 GL350151_32913 0.587103872588132 1.50222808195441 0.689521683693614 T1=T2 0 0.93495837349898 4.66115555795739 16.0514731430306 5.18080920298251 10.510631192699 +T1vsT2_GL350151_32915 T1vsT2 GL350151_32915 0.587103872588132 1.50222808195441 0.689521683693614 T1=T2 0 0.93495837349898 4.66115555795739 16.0514731430306 5.18080920298251 10.510631192699 +T1vsT2_GL350682_40710 T1vsT2 GL350682_40710 0.895281068696944 1.85997221339018 0.61536215460945 T1=T2 0 0.93495837349898 11.8785246839619 57.6693961245775 7.32689713115084 40.6813728356422 +T1vsT2_GL350737_41243 T1vsT2 GL350737_41243 0.587103872588132 1.50222808195441 0.689521683693614 T1=T2 0 0.93495837349898 4.66115555795739 16.0514731430306 5.18080920298251 10.510631192699 +T1vsT2_GL357043_46322 T1vsT2 GL357043_46322 0.733418642999605 1.6625741009678 0.660869456323149 T1=T2 0 0.93495837349898 3.31343434155413 13.0513763298296 3.09959689136328 7.70734865102163 +T1vsT2_GL366836_47437 T1vsT2 GL366836_47437 0.417609541445142 1.33571252522044 0.723430888618105 T1=T2 0 0.93495837349898 6.64462795004153 25.6873101470662 11.5235597930116 11.5718209197646 +T1vsT2_GL366836_47447 T1vsT2 GL366836_47447 0.417609541445142 1.33571252522044 0.723430888618105 T1=T2 0 0.93495837349898 6.64462795004153 25.6873101470662 11.5235597930116 11.5718209197646 +T1vsT2_GL369698_47842 T1vsT2 GL369698_47842 0.587103872588132 1.50222808195441 0.689521683693614 T1=T2 0 0.93495837349898 4.66115555795739 16.0514731430306 5.18080920298251 10.510631192699 +T1vsT2_GL369698_47844 T1vsT2 GL369698_47844 0.587103872588132 1.50222808195441 0.689521683693614 T1=T2 0 0.93495837349898 4.66115555795739 16.0514731430306 5.18080920298251 10.510631192699 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0.627748230328414 T1=T2 0 0.93495837349898 17.9980028180635 14.6499713109873 15.9702722689774 18.8509516140144 +T1vsT2_api-mir-2c T1vsT2 api-mir-2c 0.181754363245861 1.13426234623825 0.634692455442277 T1=T2 0 0.93495837349898 49.1092218181985 66.1195303451075 58.4232368367937 48.5029841502638 +T1vsT2_api-mir-3047-1 T1vsT2 api-mir-3047-1 0.296095931633425 1.22781732459597 0.750484087146718 T1=T2 0 0.93495837349898 203.230252972802 205.085416847614 183.833264399272 179.143594709771 +T1vsT2_api-mir-3047-2 T1vsT2 api-mir-3047-2 0.296095931633425 1.22781732459597 0.750484087146718 T1=T2 0 0.93495837349898 203.230252972802 205.085416847614 183.833264399272 179.143594709771 +T1vsT2_api-mir-317 T1vsT2 api-mir-317 -0.27732496959182 1.21194562256656 0.622732747300201 T1=T2 0 0.93495837349898 41.9865638867419 39.973195910454 43.1237487603943 44.9959227533424 +T1vsT2_api-mir-971 T1vsT2 api-mir-971 -0.764963349362522 1.69932682754415 0.555584012095489 T1=T2 0 0.93495837349898 10.1407187013823 19.7487913349406 15.9855065951018 16.6065473899439 +T1vsT2_api-mir-9a T1vsT2 api-mir-9a -0.180578146023801 1.13333796848703 0.644906372226478 T1=T2 0 0.93495837349898 812.438450656032 786.952021519981 879.112275743298 819.629737700813 +T1vsT2_GL349742_15837 T1vsT2 GL349742_15837 -0.077281348169236 1.05502804402967 0.803461849902489 T1=T2 0 0.973221981180124 16838.4837907878 12660.4383260529 16136.5808468847 13939.7518458743 +T1vsT2_GL349801_20413 T1vsT2 GL349801_20413 0.153975871104475 1.11263151180526 0.820001762390478 T1=T2 0 0.973221981180124 19.7476856197604 14.9856656593161 15.6293738213989 15.2885918081573 +T1vsT2_GL349919_26570 T1vsT2 GL349919_26570 0.152863259601448 1.11177377724626 0.879095701269349 T1=T2 0 0.973221981180124 25.4501089849405 87.6001270254807 33.7588466169947 60.8751850112748 +T1vsT2_GL349919_26592 T1vsT2 GL349919_26592 0.159227153934204 1.11668877202708 0.90181269576025 T1=T2 0 0.973221981180124 6.67628355694396 25.3243219280574 7.31005430057552 21.114150881836 +T1vsT2_GL350343_36473 T1vsT2 GL350343_36473 -0.0749283444860523 1.05330871911042 0.895589722255796 T1=T2 0 0.973221981180124 162.229342389252 175.96217279623 164.839570604831 180.069135472355 +T1vsT2_GL351656_44870 T1vsT2 GL351656_44870 0.16497217852783 1.1211444572499 0.894328811576083 T1=T2 0 0.973221981180124 28.7778527542278 98.2409625950879 40.9262873559157 62.7420930233442 +T1vsT2_api-mir-190 T1vsT2 api-mir-190 0.100927781362402 1.07246292996933 0.831579165776638 T1=T2 0 0.973221981180124 234.550188295047 221.766347279128 231.694995089182 205.845854702742 +T1vsT2_api-mir-2765 T1vsT2 api-mir-2765 -0.04916949539772 1.03466913274755 0.889923080357453 T1=T2 0 0.973221981180124 504.166562590324 501.98589724328 512.975079380156 507.009610435658 +T1vsT2_api-mir-279b T1vsT2 api-mir-279b 0.0531123728924739 1.03750074534084 0.860236868933231 T1=T2 0 0.973221981180124 615.057540608426 554.283861464607 593.854328320924 552.982505836701 +T1vsT2_api-mir-29 T1vsT2 api-mir-29 0.0772042188399727 1.05497164165223 0.883212197847981 T1=T2 0 0.973221981180124 105.245364266731 94.6171458451392 98.7017420713852 94.9590209808936 +T1vsT2_api-mir-3036-1 T1vsT2 api-mir-3036-1 -0.0623817873554679 1.04418821943277 0.888807544025596 T1=T2 0 0.973221981180124 355.864419414785 378.098568231729 375.340801378356 371.431717521057 +T1vsT2_api-mir-3036-2 T1vsT2 api-mir-3036-2 -0.0623817873554679 1.04418821943277 0.888807544025596 T1=T2 0 0.973221981180124 355.864419414785 378.098568231729 375.340801378356 371.431717521057 +T1vsT2_api-mir-3036-3 T1vsT2 api-mir-3036-3 -0.0616916243095803 1.04368881536419 0.890051535678869 T1=T2 0 0.973221981180124 356.02291302258 377.932084361907 375.157547119293 371.431717521057 +T1vsT2_api-mir-3036-4 T1vsT2 api-mir-3036-4 -0.0616916243095803 1.04368881536419 0.890051535678869 T1=T2 0 0.973221981180124 356.02291302258 377.932084361907 375.157547119293 371.431717521057 +T1vsT2_api-mir-3036-5 T1vsT2 api-mir-3036-5 -0.0616916243095803 1.04368881536419 0.890051535678869 T1=T2 0 0.973221981180124 356.02291302258 377.932084361907 375.157547119293 371.431717521057 +T1vsT2_api-mir-3043-1 T1vsT2 api-mir-3043-1 -0.0973262703093035 1.06978899689003 0.843794553084964 T1=T2 0 0.973221981180124 57.6997552376986 40.4424775820102 48.3999867820141 51.5082654013472 +T1vsT2_api-mir-3043-2 T1vsT2 api-mir-3043-2 -0.0973262703093035 1.06978899689003 0.843794553084964 T1=T2 0 0.973221981180124 57.6997552376986 40.4424775820102 48.3999867820141 51.5082654013472 +T1vsT2_api-mir-3043-3 T1vsT2 api-mir-3043-3 -0.0973262703093035 1.06978899689003 0.843794553084964 T1=T2 0 0.973221981180124 57.6997552376986 40.4424775820102 48.3999867820141 51.5082654013472 +T1vsT2_api-mir-3050 T1vsT2 api-mir-3050 0.0559546373818562 1.03954674822327 0.89941183195061 T1=T2 0 0.973221981180124 1142501.70015826 795661.911903157 1028755.47253531 850011.670784776 +T1vsT2_api-mir-7 T1vsT2 api-mir-7 -0.105827161281639 1.07611119606609 0.862204791982148 T1=T2 0 0.973221981180124 181.345502480794 189.343819213867 207.034028814017 173.186336148056 +T1vsT2_api-mir-993 T1vsT2 api-mir-993 -0.0412195507768203 1.02898328768674 0.906486759613487 T1=T2 0 0.973221981180124 517.095986431029 355.927103464731 451.118742022456 417.649465514703 +T1vsT2_api-mir-184a T1vsT2 api-mir-184a -0.0390450066057793 1.02743349090164 0.925330905014595 T1=T2 0 0.98141156592457 48955.440785817 35866.6670300699 45671.9115346193 39494.8236524716 +T1vsT2_api-mir-3031 T1vsT2 api-mir-3031 -0.0581845126333868 1.04115474704317 0.920478867564632 T1=T2 0 0.98141156592457 167.696215387838 188.245374819867 173.378004991112 186.623430921134 +T1vsT2_GL349643_5190 T1vsT2 GL349643_5190 -0.0426668290607514 1.03001605785128 0.961649132893672 T1=T2 0 0.998690037981219 2.73632941954876 11.030329473906 4.84406512480566 7.56335986023563 +T1vsT2_GL350151_32862 T1vsT2 GL350151_32862 -0.0193642913017359 1.01351278741972 0.982148041738455 T1=T2 0 0.998690037981219 29.3696377720969 86.6672382227376 38.7976244676746 68.4955728606815 +T1vsT2_GL350151_32866 T1vsT2 GL350151_32866 0.00225625053313585 1.00156513724646 0.998690037981219 T1=T2 0 0.998690037981219 29.8894059094906 88.817436670779 39.1623257237904 69.6964707324995 +T1vsT2_GL350151_32884 T1vsT2 GL350151_32884 -0.0424226558124306 1.02984174444643 0.965520504767908 T1=T2 0 0.998690037981219 4.60243759106838 24.7243951164809 7.06858703220598 18.050368601277 +T1vsT2_GL350151_32898 T1vsT2 GL350151_32898 -0.00976186403353511 1.00678935239405 0.987271238394924 T1=T2 0 0.998690037981219 4.60243759106838 25.6087427706126 7.06858703220598 18.2429383304036 +T1vsT2_GL350151_32906 T1vsT2 GL350151_32906 -0.00976186403353511 1.00678935239405 0.987271238394924 T1=T2 0 0.998690037981219 4.60243759106838 25.6087427706126 7.06858703220598 18.2429383304036 +T1vsT2_GL351656_44862 T1vsT2 GL351656_44862 -0.00976186403353511 1.00678935239405 0.987271238394924 T1=T2 0 0.998690037981219 4.60243759106838 25.6087427706126 7.06858703220598 18.2429383304036 +T1vsT2_api-mir-3027 T1vsT2 api-mir-3027 0.0213096232060162 1.0148803311966 0.965991192358469 T1=T2 0 0.998690037981219 404.312998546403 362.527824297402 373.591616924324 382.300123100955 +T1vsT2_api-mir-3033 T1vsT2 api-mir-3033 -0.00335649754218206 1.00232925531803 0.991314985890748 T1=T2 0 0.998690037981219 502.552807518651 332.193472624891 427.20126064499 393.371130813313 +T1vsT2_api-mir-9b T1vsT2 api-mir-9b -0.000782611364163497 1.00054261202122 0.998280719813556 T1=T2 0 0.998690037981219 436.573003510837 335.799016629453 398.350992944513 364.731785016796
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Contrasts.txt Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,8 @@ +Condition T1vsT0 T1vsT2 T1AvsT1K AvsK +T0A - 0 0 + +T1A + + + + +T1K + + - - +T2A 0 - 0 + +T2K 0 - 0 - +T3A 0 0 0 + +T3K 0 0 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Samples.txt Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,29 @@ +ID condition stage treatment +A32 T3A T3 Acetone +A34 T3A T3 Acetone +A37 T3A T3 Acetone +A39 T3A T3 Acetone +K32 T3K T3 Kinoprene +K34 T3K T3 Kinoprene +K37 T3K T3 Kinoprene +K39 T3K T3 Kinoprene +A02 T0A T0 Acetone +A06 T0A T0 Acetone +A08 T0A T0 Acetone +A09 T0A T0 Acetone +A12 T1A T1 Acetone +A16 T1A T1 Acetone +A18 T1A T1 Acetone +A19 T1A T1 Acetone +K12 T1K T1 Kinoprene +K16 T1K T1 Kinoprene +K18 T1K T1 Kinoprene +K19 T1K T1 Kinoprene +A22 T2A T2 Acetone +A24 T2A T2 Acetone +A27 T2A T2 Acetone +A29 T2A T2 Acetone +K22 T2K T2 Kinoprene +K24 T2K T2 Kinoprene +K27 T2K T2 Kinoprene +K29 T2K T2 Kinoprene
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/condition.asko.txt Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,8 @@ +Condition stage treatment +T3A T3 Acetone +T3K T3 Kinoprene +T0A T0 Acetone +T1A T1 Acetone +T1K T1 Kinoprene +T2A T2 Acetone +T2K T2 Kinoprene
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/context.asko.txt Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,15 @@ +Context has@Condition +T1 T1A +T1 T1K +T0 T0A +T2 T2A +T2 T2K +T1A T1A +T1K T1K +A T0A +A T1A +A T2A +A T3A +K T1K +K T2K +K T3K
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contrast.asko.txt Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,5 @@ +Contrast context1_of@Context context2_of@Context +T1vsT0 T1 T0 +T1vsT2 T1 T2 +T1AvsT1K T1A T1K +AvsK A K
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.csv Thu Apr 12 05:23:45 2018 -0400 @@ -0,0 +1,381 @@ +#miRNA read_count precursor total A32 A34 A37 A39 K32 K34 K37 K39 A02 A06 A08 A09 A12 A16 A18 A19 K12 K16 K18 K19 A22 A24 A27 A29 K22 K24 K27 K29 A32(norm) A34(norm) A37(norm) A39(norm) K32(norm) K34(norm) K37(norm) K39(norm) A02(norm) A06(norm) A08(norm) A09(norm) A12(norm) A16(norm) A18(norm) A19(norm) K12(norm) K16(norm) K18(norm) K19(norm) A22(norm) A24(norm) A27(norm) A29(norm) K22(norm) K24(norm) K27(norm) K29(norm) +GL349623_679 346.00 GL349623_679 346.00 16.00 1.00 11.00 6.00 4.00 14.00 4.00 16.00 7.00 49.00 1.00 10.00 8.00 18.00 23.00 18.00 0 16.00 9.00 10.00 22.00 16.00 12.00 20.00 10.00 4.00 12.00 9.00 7.39 2.57 7.74 3.64 2.74 14.77 2.56 8.85 1.51 9.55 1.39 4.27 2.92 4.37 7.78 5.12 0 4.54 4.97 5.45 3.64 4.52 2.76 7.64 2.85 4.19 4.87 2.67 +GL349624_956 13.00 GL349624_956 13.00 0 0 0 1.00 0 0 0 0 0 3.00 0 0 0 1.00 1.00 2.00 0 0 0 0 0 1.00 0 2.00 0 0 1.00 1.00 0 0 0 0.61 0 0 0 0 0 0.58 0 0 0 0.24 0.34 0.57 0 0 0 0 0 0.28 0 0.76 0 0 0.41 0.30 +GL349630_2419 2618.00 GL349630_2419 2618.00 10.00 1.00 14.00 66.00 18.00 31.00 207.00 47.00 32.00 627.00 63.00 93.00 20.00 39.00 75.00 52.00 5.00 166.00 260.00 152.00 14.00 20.00 97.00 85.00 19.00 11.00 155.00 239.00 4.62 2.57 9.85 40.02 12.32 32.71 132.53 26.01 6.91 122.25 87.69 39.70 7.30 9.48 25.36 14.81 9.44 47.06 143.62 82.78 2.32 5.65 22.31 32.45 5.41 11.51 62.88 70.79 +GL349630_2421 2618.00 GL349630_2421 2618.00 10.00 1.00 14.00 66.00 18.00 31.00 207.00 47.00 32.00 627.00 63.00 93.00 20.00 39.00 75.00 52.00 5.00 166.00 260.00 152.00 14.00 20.00 97.00 85.00 19.00 11.00 155.00 239.00 4.62 2.57 9.85 40.02 12.32 32.71 132.53 26.01 6.91 122.25 87.69 39.70 7.30 9.48 25.36 14.81 9.44 47.06 143.62 82.78 2.32 5.65 22.31 32.45 5.41 11.51 62.88 70.79 +GL349630_2423 2618.00 GL349630_2423 2618.00 10.00 1.00 14.00 66.00 18.00 31.00 207.00 47.00 32.00 627.00 63.00 93.00 20.00 39.00 75.00 52.00 5.00 166.00 260.00 152.00 14.00 20.00 97.00 85.00 19.00 11.00 155.00 239.00 4.62 2.57 9.85 40.02 12.32 32.71 132.53 26.01 6.91 122.25 87.69 39.70 7.30 9.48 25.36 14.81 9.44 47.06 143.62 82.78 2.32 5.65 22.31 32.45 5.41 11.51 62.88 70.79 +GL349630_2425 2618.00 GL349630_2425 2618.00 10.00 1.00 14.00 66.00 18.00 31.00 207.00 47.00 32.00 627.00 63.00 93.00 20.00 39.00 75.00 52.00 5.00 166.00 260.00 152.00 14.00 20.00 97.00 85.00 19.00 11.00 155.00 239.00 4.62 2.57 9.85 40.02 12.32 32.71 132.53 26.01 6.91 122.25 87.69 39.70 7.30 9.48 25.36 14.81 9.44 47.06 143.62 82.78 2.32 5.65 22.31 32.45 5.41 11.51 62.88 70.79 +GL349630_2427 250.00 GL349630_2427 250.00 1.00 0 3.00 7.00 2.00 5.00 16.00 9.00 0 54.00 15.00 7.00 3.00 0 9.00 0 1.00 14.00 36.00 14.00 0 1.00 9.00 6.00 0 3.00 14.00 21.00 0.46 0 2.11 4.24 1.37 5.28 10.24 4.98 0 10.53 20.88 2.99 1.09 0 3.04 0 1.89 3.97 19.89 7.62 0 0.28 2.07 2.29 0 3.14 5.68 6.22 +GL349633_2878 13.00 GL349633_2878 13.00 1.00 0 0 0 1.00 0 0 1.00 1.00 1.00 0 0 2.00 0 0 0 1.00 0 1.00 0 1.00 2.00 0 0 0 0 1.00 0 0.46 0 0 0 0.68 0 0 0.55 0.22 0.19 0 0 0.73 0 0 0 1.89 0 0.55 0 0.17 0.56 0 0 0 0 0.41 0 +GL349634_3207 107.00 GL349634_3207 107.00 4.00 0 0 5.00 1.00 4.00 4.00 2.00 8.00 8.00 1.00 6.00 1.00 8.00 3.00 5.00 0 7.00 5.00 3.00 3.00 7.00 3.00 3.00 8.00 2.00 1.00 5.00 1.85 0 0 3.03 0.68 4.22 2.56 1.11 1.73 1.56 1.39 2.56 0.36 1.94 1.01 1.42 0 1.98 2.76 1.63 0.50 1.98 0.69 1.15 2.28 2.09 0.41 1.48 +GL349634_3209 271.00 GL349634_3209 271.00 6.00 5.00 6.00 19.00 5.00 1.00 13.00 7.00 8.00 8.00 3.00 13.00 0 13.00 11.00 20.00 2.00 16.00 12.00 12.00 18.00 8.00 9.00 18.00 15.00 2.00 10.00 11.00 2.77 12.85 4.22 11.52 3.42 1.06 8.32 3.87 1.73 1.56 4.18 5.55 0 3.16 3.72 5.69 3.78 4.54 6.63 6.54 2.98 2.26 2.07 6.87 4.27 2.09 4.06 3.26 +GL349637_3676 15.00 GL349637_3676 15.00 0 0 1.00 0 0 0 3.00 0 3.00 1.00 0 0 0 0 0 2.00 0 1.00 2.00 0 0 0 1.00 0 0 0 0 1.00 0 0 0.70 0 0 0 1.92 0 0.65 0.19 0 0 0 0 0 0.57 0 0.28 1.10 0 0 0 0.23 0 0 0 0 0.30 +GL349639_4112 92.00 GL349639_4112 92.00 1.00 1.00 3.00 0 1.00 3.00 0 3.00 4.00 17.00 5.00 7.00 0 2.00 8.00 1.00 0 8.00 2.00 3.00 6.00 3.00 4.00 4.00 0 1.00 2.00 3.00 0.46 2.57 2.11 0 0.68 3.17 0 1.66 0.86 3.31 6.96 2.99 0 0.49 2.70 0.28 0 2.27 1.10 1.63 0.99 0.85 0.92 1.53 0 1.05 0.81 0.89 +GL349640_4529 113.00 GL349640_4529 113.00 0 2.00 6.00 3.00 6.00 1.00 9.00 8.00 5.00 5.00 3.00 3.00 0 2.00 5.00 8.00 0 4.00 7.00 4.00 1.00 10.00 8.00 4.00 3.00 1.00 2.00 3.00 0 5.14 4.22 1.82 4.11 1.06 5.76 4.43 1.08 0.97 4.18 1.28 0 0.49 1.69 2.28 0 1.13 3.87 2.18 0.17 2.82 1.84 1.53 0.85 1.05 0.81 0.89 +GL349641_4750 18.00 GL349641_4750 18.00 0 0 0 0 1.00 0 1.00 0 2.00 0 1.00 0 0 2.00 3.00 0 0 3.00 1.00 1.00 0 0 0 1.00 0 0 2.00 0 0 0 0 0 0.68 0 0.64 0 0.43 0 1.39 0 0 0.49 1.01 0 0 0.85 0.55 0.54 0 0 0 0.38 0 0 0.81 0 +GL349642_4945 6995.00 GL349642_4945 6995.00 36.00 4.00 33.00 115.00 54.00 97.00 432.00 90.00 64.00 1830.00 232.00 277.00 77.00 128.00 168.00 145.00 12.00 478.00 824.00 421.00 28.00 76.00 236.00 166.00 79.00 61.00 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7.71 2.11 3.64 4.11 5.28 3.84 4.98 0.65 0.78 0 0.85 0 1.46 2.70 2.85 1.89 2.55 1.66 0.54 1.49 3.95 1.84 6.11 3.70 5.23 3.25 4.15 +api-miR-252a 10859.00 api-mir-252a 10859.00 390.00 98.00 300.00 290.00 226.00 260.00 348.00 340.00 499.00 430.00 131.00 290.00 284.00 752.00 620.00 581.00 61.00 512.00 270.00 255.00 798.00 498.00 637.00 421.00 476.00 168.00 446.00 478.00 180.16 251.91 211.06 175.84 154.67 274.31 222.81 188.15 107.78 83.84 182.35 123.79 103.66 182.73 209.61 165.42 115.23 145.15 149.15 138.88 131.96 140.59 146.49 160.72 135.45 175.82 180.92 141.59 +api-miR-252b 2211.00 api-mir-252b 2211.00 70.00 35.00 76.00 73.00 63.00 68.00 80.00 71.00 193.00 44.00 20.00 39.00 27.00 142.00 101.00 130.00 17.00 73.00 69.00 63.00 130.00 96.00 94.00 103.00 106.00 45.00 81.00 102.00 32.34 89.97 53.47 44.26 43.12 71.74 51.22 39.29 41.69 8.58 27.84 16.65 9.85 34.50 34.15 37.01 32.11 20.70 38.12 34.31 21.50 27.10 21.62 39.32 30.16 47.09 32.86 30.21 +api-miR-263a 2893540.00 api-mir-263a 2893540.00 137589.00 18501.00 63816.00 61237.00 80682.00 37336.00 67561.00 67343.00 192201.00 113910.00 25162.00 63661.00 117427.00 138660.00 104804.00 100815.00 31386.00 121081.00 57141.00 54798.00 352437.00 195906.00 165728.00 80220.00 213992.00 35983.00 87902.00 106261.00 63559.46 47557.23 44896.26 37130.46 55216.37 39390.24 43256.95 37266.80 41513.23 22208.97 35025.06 27174.36 42859.60 33693.34 35432.36 28703.90 59287.44 34326.06 31564.80 29843.79 58279.90 55307.09 38113.07 30624.20 60891.73 37656.93 35658.04 31475.29 +api-miR-263b 32641.00 api-mir-263b 32641.00 1574.00 141.00 625.00 555.00 851.00 319.00 651.00 574.00 3148.00 1523.00 330.00 863.00 1398.00 1337.00 1132.00 1002.00 361.00 954.00 633.00 546.00 4285.00 2481.00 1493.00 832.00 3090.00 317.00 791.00 835.00 727.11 362.44 439.70 336.52 582.40 336.55 416.81 317.64 679.93 296.94 459.35 368.38 510.26 324.88 382.71 285.29 681.92 270.46 349.67 297.36 708.58 700.42 343.35 317.62 879.26 331.75 320.87 247.33 +api-miR-275 1721.00 api-mir-275 1721.00 47.00 15.00 45.00 60.00 58.00 58.00 68.00 59.00 80.00 90.00 21.00 48.00 26.00 83.00 50.00 102.00 26.00 72.00 52.00 75.00 110.00 58.00 77.00 63.00 95.00 42.00 71.00 70.00 21.71 38.56 31.66 36.38 39.69 61.19 43.54 32.65 17.28 17.55 29.23 20.49 9.49 20.17 16.90 29.04 49.11 20.41 28.72 40.85 18.19 16.37 17.71 24.05 27.03 43.95 28.80 20.73 +api-miR-276 1220289.00 api-mir-276 1220289.00 34785.00 11734.00 38169.00 48007.00 23633.00 35793.00 43432.00 56601.00 48772.00 55933.00 12269.00 31181.00 28884.00 61398.00 48430.00 65530.00 7604.00 59706.00 34250.00 34580.00 72666.00 45011.00 65199.00 62255.00 46867.00 21010.00 50634.00 75956.00 16068.99 30162.51 26852.91 29108.58 16173.73 37762.34 27807.99 31322.30 10534.20 10905.23 17078.23 13309.94 10542.35 14919.25 16373.32 18657.61 14363.78 16926.45 18919.77 18832.77 12016.24 12707.25 14994.05 23766.01 13336.07 21987.38 20540.03 22498.73 +api-miR-2765 13313.00 api-mir-2765 13313.00 197.00 69.00 305.00 245.00 120.00 191.00 351.00 268.00 901.00 1159.00 246.00 627.00 313.00 611.00 589.00 803.00 116.00 611.00 526.00 536.00 795.00 495.00 642.00 586.00 526.00 239.00 521.00 725.00 91.00 177.37 214.58 148.55 82.12 201.51 224.73 148.31 194.61 225.97 342.43 267.64 114.24 148.47 199.13 228.63 219.12 173.22 290.56 291.91 131.46 139.75 147.64 223.71 149.67 250.12 211.35 214.75 +api-miR-277 2546.00 api-mir-277 2546.00 83.00 25.00 70.00 118.00 54.00 91.00 90.00 107.00 103.00 138.00 33.00 66.00 64.00 117.00 111.00 141.00 8.00 102.00 84.00 71.00 150.00 94.00 138.00 116.00 82.00 48.00 92.00 150.00 38.34 64.26 49.25 71.55 36.96 96.01 57.62 59.21 22.25 26.91 45.94 28.17 23.36 28.43 37.53 40.15 15.11 28.92 46.40 38.67 24.80 26.54 31.74 44.28 23.33 50.23 37.32 44.43 +api-miR-278 1551.00 api-mir-278 1551.00 111.00 64.00 89.00 117.00 93.00 118.00 75.00 118.00 85.00 67.00 18.00 17.00 28.00 55.00 63.00 35.00 16.00 25.00 46.00 25.00 42.00 42.00 23.00 32.00 49.00 21.00 31.00 46.00 51.28 164.51 62.61 70.94 63.65 124.49 48.02 65.30 18.36 13.06 25.06 7.26 10.22 13.36 21.30 9.97 30.22 7.09 25.41 13.62 6.95 11.86 5.29 12.22 13.94 21.98 12.58 13.63 +api-miR-2796 32.00 api-mir-2796 32.00 1.00 0 2.00 2.00 0 2.00 4.00 2.00 0 3.00 1.00 0 2.00 0 0 1.00 0 1.00 0 0 0 3.00 2.00 0 2.00 0 1.00 3.00 0.46 0 1.41 1.21 0 2.11 2.56 1.11 0 0.58 1.39 0 0.73 0 0 0.28 0 0.28 0 0 0 0.85 0.46 0 0.57 0 0.41 0.89 +api-miR-279a 44409.00 api-mir-279a 44409.00 838.00 219.00 964.00 1138.00 581.00 728.00 1261.00 1228.00 2904.00 4275.00 747.00 2106.00 1150.00 2287.00 1950.00 2926.00 214.00 2348.00 1733.00 1727.00 2107.00 1340.00 1940.00 1710.00 1428.00 590.00 1604.00 2366.00 387.12 562.94 678.20 690.02 397.62 768.05 807.37 679.56 627.23 833.49 1039.81 898.97 419.74 555.72 659.26 833.09 404.24 665.65 957.31 940.55 348.42 378.30 446.15 652.80 406.34 617.45 650.67 700.83 +api-miR-279b 16338.00 api-mir-279b 16338.00 361.00 105.00 449.00 517.00 269.00 295.00 520.00 520.00 928.00 1118.00 238.00 612.00 339.00 828.00 658.00 1087.00 90.00 896.00 672.00 648.00 843.00 563.00 806.00 706.00 594.00 232.00 579.00 865.00 166.76 269.90 315.88 313.48 184.10 311.23 332.94 287.76 200.44 217.98 331.29 261.24 123.73 201.20 222.46 309.49 170.01 254.01 371.21 352.91 139.40 158.94 185.36 269.52 169.02 242.79 234.88 256.22 +api-miR-281 451.00 api-mir-281 451.00 16.00 7.00 13.00 23.00 5.00 18.00 23.00 32.00 13.00 13.00 5.00 3.00 12.00 29.00 17.00 24.00 4.00 23.00 6.00 14.00 16.00 13.00 25.00 25.00 14.00 11.00 21.00 26.00 7.39 17.99 9.15 13.95 3.42 18.99 14.73 17.71 2.81 2.53 6.96 1.28 4.38 7.05 5.75 6.83 7.56 6.52 3.31 7.62 2.65 3.67 5.75 9.54 3.98 11.51 8.52 7.70 +api-miR-29 2585.00 api-mir-29 2585.00 37.00 10.00 65.00 60.00 28.00 41.00 69.00 73.00 173.00 95.00 50.00 119.00 43.00 145.00 141.00 182.00 17.00 134.00 118.00 110.00 98.00 105.00 173.00 105.00 105.00 35.00 130.00 124.00 17.09 25.71 45.73 36.38 19.16 43.26 44.18 40.40 37.37 18.52 69.60 50.80 15.69 35.23 47.67 51.82 32.11 37.99 65.18 59.91 16.21 29.64 39.79 40.08 29.88 36.63 52.74 36.73 +api-miR-2a 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12.00 110.00 71.00 72.00 66.00 56.00 85.00 79.00 37.00 20.00 63.00 90.00 14.32 30.85 14.07 18.80 13.69 21.10 23.05 19.92 25.05 41.92 44.54 36.71 9.12 19.68 16.90 22.49 22.67 31.18 39.22 39.21 10.91 15.81 19.55 30.16 10.53 20.93 25.56 26.66 +api-miR-3015a 72.00 api-mir-3015a-1 72.00 5.00 2.00 7.00 3.00 3.00 4.00 7.00 3.00 1.00 3.00 2.00 1.00 2.00 0 1.00 1.00 3.00 3.00 2.00 5.00 1.00 1.00 1.00 3.00 0 3.00 0 5.00 2.31 5.14 4.92 1.82 2.05 4.22 4.48 1.66 0.22 0.58 2.78 0.43 0.73 0 0.34 0.28 5.67 0.85 1.10 2.72 0.17 0.28 0.23 1.15 0 3.14 0 1.48 +api-miR-3015a 72.00 api-mir-3015a-2 72.00 5.00 2.00 7.00 3.00 3.00 4.00 7.00 3.00 1.00 3.00 2.00 1.00 2.00 0 1.00 1.00 3.00 3.00 2.00 5.00 1.00 1.00 1.00 3.00 0 3.00 0 5.00 2.31 5.14 4.92 1.82 2.05 4.22 4.48 1.66 0.22 0.58 2.78 0.43 0.73 0 0.34 0.28 5.67 0.85 1.10 2.72 0.17 0.28 0.23 1.15 0 3.14 0 1.48 +api-miR-3015b 90.00 api-mir-3015b 90.00 5.00 4.00 6.00 4.00 2.00 3.00 5.00 3.00 3.00 5.00 4.00 2.00 4.00 6.00 2.00 4.00 1.00 0 2.00 3.00 4.00 1.00 4.00 4.00 3.00 1.00 2.00 3.00 2.31 10.28 4.22 2.43 1.37 3.17 3.20 1.66 0.65 0.97 5.57 0.85 1.46 1.46 0.68 1.14 1.89 0 1.10 1.63 0.66 0.28 0.92 1.53 0.85 1.05 0.81 0.89 +api-miR-3015c 218.00 api-mir-3015c 218.00 3.00 1.00 6.00 5.00 4.00 6.00 6.00 9.00 9.00 13.00 2.00 15.00 5.00 10.00 4.00 14.00 1.00 19.00 6.00 9.00 10.00 11.00 16.00 14.00 2.00 3.00 7.00 8.00 1.39 2.57 4.22 3.03 2.74 6.33 3.84 4.98 1.94 2.53 2.78 6.40 1.82 2.43 1.35 3.99 1.89 5.39 3.31 4.90 1.65 3.11 3.68 5.34 0.57 3.14 2.84 2.37 +api-miR-3016 382.00 api-mir-3016 382.00 6.00 0 3.00 6.00 1.00 5.00 6.00 4.00 40.00 89.00 13.00 19.00 6.00 6.00 21.00 13.00 3.00 32.00 28.00 28.00 8.00 5.00 4.00 9.00 6.00 0 11.00 10.00 2.77 0 2.11 3.64 0.68 5.28 3.84 2.21 8.64 17.35 18.10 8.11 2.19 1.46 7.10 3.70 5.67 9.07 15.47 15.25 1.32 1.41 0.92 3.44 1.71 0 4.46 2.96 +api-miR-3017a 18.00 api-mir-3017a 18.00 2.00 0 2.00 3.00 1.00 0 0 1.00 0 0 0 0 0 0 0 0 1.00 1.00 0 0 1.00 0 1.00 1.00 0 1.00 2.00 1.00 0.92 0 1.41 1.82 0.68 0 0 0.55 0 0 0 0 0 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1.00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.41 0 +api-miR-3020 80.00 api-mir-3020 80.00 1.00 0 4.00 4.00 2.00 1.00 3.00 5.00 2.00 8.00 1.00 0 1.00 2.00 0 4.00 0 6.00 2.00 2.00 1.00 5.00 7.00 7.00 0 1.00 5.00 6.00 0.46 0 2.81 2.43 1.37 1.06 1.92 2.77 0.43 1.56 1.39 0 0.36 0.49 0 1.14 0 1.70 1.10 1.09 0.17 1.41 1.61 2.67 0 1.05 2.03 1.78 +api-miR-3021 3.00 api-mir-3021-1 3.00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.00 1.00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.33 0.28 0 0 0 0 0 0 +api-miR-3021 3.00 api-mir-3021-2 3.00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.00 1.00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.33 0.28 0 0 0 0 0 0 +api-miR-3021 3.00 api-mir-3021-3 3.00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.00 1.00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.33 0.28 0 0 0 0 0 0 +api-miR-3022 29.00 api-mir-3022 29.00 1.00 0 1.00 1.00 0 3.00 2.00 1.00 1.00 0 1.00 1.00 0 2.00 2.00 1.00 0 2.00 1.00 0 1.00 2.00 0 1.00 1.00 0 1.00 3.00 0.46 0 0.70 0.61 0 3.17 1.28 0.55 0.22 0 1.39 0.43 0 0.49 0.68 0.28 0 0.57 0.55 0 0.17 0.56 0 0.38 0.28 0 0.41 0.89 +api-miR-3023 42.00 api-mir-3023 42.00 0 0 0 3.00 0 1.00 5.00 0 0 2.00 0 0 0 3.00 2.00 0 0 3.00 4.00 4.00 1.00 0 2.00 4.00 0 1.00 3.00 4.00 0 0 0 1.82 0 1.06 3.20 0 0 0.39 0 0 0 0.73 0.68 0 0 0.85 2.21 2.18 0.17 0 0.46 1.53 0 1.05 1.22 1.18 +api-miR-3024 771.00 api-mir-3024 771.00 9.00 1.00 2.00 7.00 2.00 3.00 8.00 9.00 73.00 224.00 18.00 49.00 33.00 25.00 39.00 35.00 4.00 69.00 28.00 38.00 9.00 9.00 15.00 13.00 16.00 6.00 8.00 19.00 4.16 2.57 1.41 4.24 1.37 3.17 5.12 4.98 15.77 43.67 25.06 20.92 12.04 6.07 13.19 9.97 7.56 19.56 15.47 20.70 1.49 2.54 3.45 4.96 4.55 6.28 3.25 5.63 +api-miR-3025 246.00 api-mir-3025 246.00 4.00 5.00 7.00 5.00 7.00 6.00 8.00 5.00 3.00 18.00 10.00 2.00 4.00 16.00 11.00 13.00 0 19.00 9.00 4.00 12.00 4.00 11.00 10.00 17.00 6.00 13.00 17.00 1.85 12.85 4.92 3.03 4.79 6.33 5.12 2.77 0.65 3.51 13.92 0.85 1.46 3.89 3.72 3.70 0 5.39 4.97 2.18 1.98 1.13 2.53 3.82 4.84 6.28 5.27 5.04 +api-miR-3026 343.00 api-mir-3026 343.00 12.00 2.00 8.00 14.00 4.00 5.00 11.00 15.00 13.00 10.00 6.00 5.00 12.00 20.00 16.00 25.00 2.00 17.00 8.00 7.00 17.00 11.00 31.00 13.00 12.00 7.00 19.00 21.00 5.54 5.14 5.63 8.49 2.74 5.28 7.04 8.30 2.81 1.95 8.35 2.13 4.38 4.86 5.41 7.12 3.78 4.82 4.42 3.81 2.81 3.11 7.13 4.96 3.41 7.33 7.71 6.22 +api-miR-3027 10508.00 api-mir-3027 10508.00 184.00 90.00 326.00 306.00 175.00 238.00 305.00 346.00 926.00 575.00 179.00 459.00 205.00 690.00 498.00 503.00 92.00 469.00 360.00 316.00 460.00 458.00 453.00 417.00 488.00 169.00 376.00 445.00 85.00 231.35 229.35 185.54 119.76 251.09 195.28 191.47 200.01 112.11 249.16 195.93 74.82 167.66 168.36 143.21 173.79 132.96 198.86 172.10 76.07 129.30 104.18 159.19 138.86 176.86 152.53 131.81 +api-miR-3028 0.00 api-mir-3028 0.00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +api-miR-3029 7.00 api-mir-3029 7.00 0 0 0 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41.39 5.29 13.55 10.58 16.03 11.10 23.02 15.41 13.03 +api-miR-92b 9834.00 api-mir-92b-1 9834.00 169.00 33.00 162.00 222.00 112.00 114.00 178.00 175.00 951.00 1372.00 208.00 618.00 238.00 459.00 472.00 610.00 56.00 571.00 420.00 436.00 360.00 274.00 335.00 311.00 257.00 129.00 224.00 368.00 78.07 84.83 113.97 134.61 76.65 120.27 113.97 96.84 205.41 267.50 289.53 263.80 86.87 111.53 159.57 173.68 105.78 161.88 232.01 237.45 59.53 77.35 77.04 118.73 73.13 135.00 90.87 109.00 +api-miR-92b 9834.00 api-mir-92b-2 9834.00 169.00 33.00 162.00 222.00 112.00 114.00 178.00 175.00 951.00 1372.00 208.00 618.00 238.00 459.00 472.00 610.00 56.00 571.00 420.00 436.00 360.00 274.00 335.00 311.00 257.00 129.00 224.00 368.00 78.07 84.83 113.97 134.61 76.65 120.27 113.97 96.84 205.41 267.50 289.53 263.80 86.87 111.53 159.57 173.68 105.78 161.88 232.01 237.45 59.53 77.35 77.04 118.73 73.13 135.00 90.87 109.00 +api-miR-965 268.00 api-mir-965 268.00 2.00 4.00 10.00 8.00 7.00 12.00 15.00 12.00 19.00 10.00 3.00 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194.88 158.37 102.56 149.93 175.13 158.59 143.56 135.51 185.05 179.72 109.14 98.81 109.24 184.77 99.88 175.82 159.42 167.95 +api-miR-iab-4 251.00 api-mir-iab-4 251.00 5.00 1.00 10.00 4.00 6.00 1.00 6.00 6.00 11.00 21.00 8.00 18.00 4.00 17.00 11.00 21.00 3.00 15.00 6.00 10.00 10.00 7.00 10.00 11.00 6.00 0 7.00 16.00 2.31 2.57 7.04 2.43 4.11 1.06 3.84 3.32 2.38 4.09 11.14 7.68 1.46 4.13 3.72 5.98 5.67 4.25 3.31 5.45 1.65 1.98 2.30 4.20 1.71 0 2.84 4.74