| Previous changeset 11:24ac6f93cc3e (2017-05-11) Next changeset 13:3735f4bd0a2d (2017-06-12) |
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Commit message:
Uploaded |
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modified:
findDMR/.Rhistory findDMR/findDMR.R findDMR/findDMR.xml |
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removed:
findDMR/test-data/._input.csv findDMR/test-data/DMR.bed findDMR/test-data/MetaTable.csv findDMR/test-data/input.csv findDMR/tool_dependencies.xml |
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| diff -r 24ac6f93cc3e -r 083895dbc289 findDMR/.Rhistory --- a/findDMR/.Rhistory Thu May 11 11:26:02 2017 -0400 +++ b/findDMR/.Rhistory Mon Jun 12 11:05:04 2017 -0400 |
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| @@ -1,200 +1,1 @@ -clusterSize=2 -class(clusterSize) -type(clusterSize) -require("minfi", quietly = TRUE) -??getGenomicRatioSetFromGEO -getGenomicRatioSetFromGEO -getwd() -GEODataTable <- getGEO(GSE51547) -require("BiocGenerics", quietly = TRUE) -require("data.table", quietly = TRUE) -require("GEOquery", quietly = TRUE) -require("rtracklayer", quietly = TRUE) -require("FDb.InfiniumMethylation.hg19", quietly = TRUE) -GEODataTable <- getGEO(GSE51547) -GEODataTable <- getGEO("GSE51547") -IlmnIDTable <- Table(GEODataTable) -MetaData <- data.frame(Meta(GEODataTable)) -IlmnIDTable <- Table(GEODataTable) -GEODataTable -GSE<-"GSE51547" -function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k", -annotation = .default.450k.annotation, what = c("Beta", "M"), -mergeManifest = FALSE, i = 1) -{ -what <- match.arg(what) -if (is.null(GSE) && is.null(path)) -stop("Either GSE or path must be supplied.") -if (!is.null(GSE)) -gset <- GEOquery::getGEO(GSE) -else gset <- GEOquery::getGEO(filename = file.path(path, -list.files(path, pattern = ".soft"))) -if (length(gset) == 0) -stop("Empty list retrieved from GEO.") -if (length(gset) > 1) { -warning("More than one ExpressionSet found:\n", names(gset), -"\nUsing entry ", i) -gset <- gset[[i]] -} -else gset <- gset[[1]] -platform <- annotation(gset) -if (platform != "GPL13534") -warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.", -platform)) -if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) < -0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1)) -warning("Values outside [0,1] detected. 'what' argument should not be Beta.") -ann <- .getAnnotationString(c(array = array, annotation = annotation)) -if (!require(ann, character.only = TRUE)) -stop(sprintf("cannot load annotation package %s", ann)) -object <- get(ann) -gr <- getLocations(object, mergeManifest = mergeManifest, -orderByLocation = TRUE) -locusNames <- names(gr) -sampleNames(gset) <- gset$title -common <- intersect(locusNames, fData(gset)$Name) -if (length(common) == 0) -stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.") -ind1 <- match(common, fData(gset)$Name) -ind2 <- match(common, locusNames) -preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details")) -if (what == "Beta") { -out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1, -, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset), -annotation = c(array = array, annotation = annotation), -preprocessMethod = preprocessing) -} -else { -out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL, -M = exprs(gset)[ind1, , drop = FALSE], CN = NULL, -pData = pData(gset), annotation = c(array = array, -annotation = annotation), preprocessMethod = preprocessing) -} -return(out) -} -<environment: namespace:minfi> -function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k", -annotation = .default.450k.annotation, what = c("Beta", "M"), -mergeManifest = FALSE, i = 1) -{ -what <- match.arg(what) -if (is.null(GSE) && is.null(path)) -stop("Either GSE or path must be supplied.") -if (!is.null(GSE)) -gset <- GEOquery::getGEO(GSE) -else gset <- GEOquery::getGEO(filename = file.path(path, -list.files(path, pattern = ".soft"))) -if (length(gset) == 0) -stop("Empty list retrieved from GEO.") -if (length(gset) > 1) { -warning("More than one ExpressionSet found:\n", names(gset), -"\nUsing entry ", i) -gset <- gset[[i]] -} -else gset <- gset[[1]] -platform <- annotation(gset) -if (platform != "GPL13534") -warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.", -platform)) -if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) < -0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1)) -warning("Values outside [0,1] detected. 'what' argument should not be Beta.") -ann <- .getAnnotationString(c(array = array, annotation = annotation)) -if (!require(ann, character.only = TRUE)) -stop(sprintf("cannot load annotation package %s", ann)) -object <- get(ann) -gr <- getLocations(object, mergeManifest = mergeManifest, -orderByLocation = TRUE) -locusNames <- names(gr) -sampleNames(gset) <- gset$title -common <- intersect(locusNames, fData(gset)$Name) -if (length(common) == 0) -stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.") -ind1 <- match(common, fData(gset)$Name) -ind2 <- match(common, locusNames) -preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details")) -if (what == "Beta") { -out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1, -, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset), -annotation = c(array = array, annotation = annotation), -preprocessMethod = preprocessing) -} -else { -out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL, -M = exprs(gset)[ind1, , drop = FALSE], CN = NULL, -pData = pData(gset), annotation = c(array = array, -annotation = annotation), preprocessMethod = preprocessing) -} -return(out) -} -GSE<-"GSE51547" -function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k", -annotation = .default.450k.annotation, what = c("Beta", "M"), -mergeManifest = FALSE, i = 1) -{ -what <- match.arg(what) -if (is.null(GSE) && is.null(path)) -stop("Either GSE or path must be supplied.") -if (!is.null(GSE)) -gset <- GEOquery::getGEO(GSE) -else gset <- GEOquery::getGEO(filename = file.path(path, -list.files(path, pattern = ".soft"))) -if (length(gset) == 0) -stop("Empty list retrieved from GEO.") -if (length(gset) > 1) { -warning("More than one ExpressionSet found:\n", names(gset), -"\nUsing entry ", i) -gset <- gset[[i]] -} -else gset <- gset[[1]] -platform <- annotation(gset) -if (platform != "GPL13534") -warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.", -platform)) -if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) < -0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1)) -warning("Values outside [0,1] detected. 'what' argument should not be Beta.") -ann <- .getAnnotationString(c(array = array, annotation = annotation)) -if (!require(ann, character.only = TRUE)) -stop(sprintf("cannot load annotation package %s", ann)) -object <- get(ann) -gr <- getLocations(object, mergeManifest = mergeManifest, -orderByLocation = TRUE) -locusNames <- names(gr) -sampleNames(gset) <- gset$title -common <- intersect(locusNames, fData(gset)$Name) -if (length(common) == 0) -stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.") -ind1 <- match(common, fData(gset)$Name) -ind2 <- match(common, locusNames) -preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details")) -if (what == "Beta") { -out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1, -, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset), -annotation = c(array = array, annotation = annotation), -preprocessMethod = preprocessing) -} -else { -out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL, -M = exprs(gset)[ind1, , drop = FALSE], CN = NULL, -pData = pData(gset), annotation = c(array = array, -annotation = annotation), preprocessMethod = preprocessing) -} -return(out) -} -out -GSE<-"GSE51547" -gset <- getGEO(GSE) -ann <- .getAnnotationString(c(array = array, annotation = annotation)) -platform <- annotation(gset) -hm450.hg19 <- getPlatform() -IlmnInfo <- -data.table( -IlmnID = names(hm450.hg19), -CHR = as.data.frame(hm450.hg19@seqnames)$value, -BP = as.numeric(hm450.hg19@elementMetadata$probeStart) -) -IlmnIDTable <- Table(gset) -??getGenomicRatioSetFromGEO() -getGenomicRatioSetFromGEO() -getGenomicRatioSetFromGEO +??fread |
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| diff -r 24ac6f93cc3e -r 083895dbc289 findDMR/findDMR.R --- a/findDMR/findDMR.R Thu May 11 11:26:02 2017 -0400 +++ b/findDMR/findDMR.R Mon Jun 12 11:05:04 2017 -0400 |
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| @@ -1,42 +1,36 @@ -require("BiocGenerics", quietly = TRUE) -require("data.table", quietly = TRUE) -require("bumphunter", quietly = TRUE) +require("minfi", quietly = TRUE) + +options(warn = -1) +options("download.file.method"="wget") args <- commandArgs(trailingOnly = TRUE) -GSMTable = args[1] -platform = args[2] -Data_Table = args[3] -cutoff = as.numeric(args[4]) -clusterSize = as.numeric(args[5]) -DMR = args[6] +input1 = args[1] +input2 = args[2] +cutoff = as.numeric(args[3]) +B = as.numeric(args[4]) +pickCutoffQ = as.numeric(args[5]) +output1 = args[6] +output2 = args[7] -TAB = fread(GSMTable) - -IlmnInfo = fread(platform) +GRset <- get(load(input1)) -gmSet = fread(Data_Table) +pheno <- fread(input2) -# bumphunter Run with processed data -designMatrix <- model.matrix( ~ TAB$Phenotype) +designMatrix <- model.matrix(~ pheno$Phenotype) -bumps <- bumphunter( - as.matrix(gmSet), - design = designMatrix, - pos = IlmnInfo$BP, - cutoff = cutoff, - chr = IlmnInfo$CHR -) +dmrs <- bumphunter(GRset, design = designMatrix, + cutoff =cutoff, B=B, type="Beta", pickCutoff=TRUE, + pickCutoffQ=pickCutoffQ) + +DMRTable <- dmrs$table + +write.table(DMRTable, output1) -# choose DMR's of a certain length threshold -DMRTable <- bumps$table[which(bumps$table$L >= clusterSize), ] -DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end) - +sign=sign(DMRTable$value) -write.table( - DMRInfo, - DMR, - quote = F, - sep = "\t", - row.names = F, - col.names = F -) +sign[sign==-1]="-" +sign[sign==1]="+" + +dmr_track<-cbind(as.character(DMRTable$chr),DMRTable$start,DMRTable$end,sign) + +write.table(dmr_track,output2,quote = FALSE, sep = "\t\t\t\t",row.names = FALSE, col.names = FALSE,append=TRUE) \ No newline at end of file |
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| diff -r 24ac6f93cc3e -r 083895dbc289 findDMR/findDMR.xml --- a/findDMR/findDMR.xml Thu May 11 11:26:02 2017 -0400 +++ b/findDMR/findDMR.xml Mon Jun 12 11:05:04 2017 -0400 |
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| @@ -1,57 +1,34 @@ -<tool id="DMR" name="findDMR" version="1.16.2"> - <description> -from series of samples - </description> +<tool id="findDMR" name="findDMR" version="1.16.2"> <requirements> - <requirement type= "package" version="0.0.1">450kdependency</requirement> - <requirement type="package" version="3.2.1">R</requirement> - </requirements> + <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement> +</requirements> <stdio> <exit_code range="1:" /> </stdio> - <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command> + <command> Rscript $__tool_directory__/findDMR.R "$input1" "$input2" "$output" </command> <inputs> - <param optional="false" format="txt" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable"> - <validator type="empty_field" message="This field is required."/> - </param> - <param optional="false" format="txt" name="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform"> - <validator type="empty_field" message="This field is required."/> - </param> - <param optional="false" format="txt" name="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table"> - <validator type="empty_field" message="This field is required."/> - </param> - <param name="cutoff" type="float" value="" - label="Enter cutoff size (number)" - help="e.g. '0.2'" > - </param> - <param name="clusterSize" type="float" value="" - label="Enter cluster size (number)" - help="e.g. '2'" > - </param> + <param name="input1" format="Rdata" label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/> + <param name="input2" format="txt" label="PhenoTab.txt" help="ID and Phenotype table"/> </inputs> <outputs> - <data format="bed" name="DMR" label="DMR.bed"/> + <data format="txt" name="output" label="findDMR.txt"/> </outputs> <tests> <test> <param name="test"> - <element name="test-data"> - <collection type="data"> - <element name="GSMTable" value="test-data/input.txt"/> - <element name="platform" value="test-data/platform.txt"/> - <element name="Data_Table" value="test-data/Data_Table.txt"/> - <element name="cutoff" value="0.2"/> - <element name="clusterSize" value="2"/> + <element name="test-data"/> + <collection type="data"> + <element format="Rdata" name="input1" label="test-data/GenomicRatioSet.Rdata"/> + <element format="txt" name="input2" label="test-data/PhenoTab.txt"/> </collection> - </element> </param> - <output format="bed" name="DMR" label="test-data/DMR.bed"/> + <output format="txt" name="output" label="test-data/findDMR.txt"/> </test> </tests> <help> -**Description** +Identify CpGs where methylation is associated with a continuous or categorical phenotype. </help> <citations> -DMR +Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369. </citations> </tool> |
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| diff -r 24ac6f93cc3e -r 083895dbc289 findDMR/test-data/._input.csv |
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| Binary file findDMR/test-data/._input.csv has changed |
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| diff -r 24ac6f93cc3e -r 083895dbc289 findDMR/test-data/DMR.bed --- a/findDMR/test-data/DMR.bed Thu May 11 11:26:02 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,9881 +0,0 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|
| b |
| diff -r 24ac6f93cc3e -r 083895dbc289 findDMR/test-data/MetaTable.csv --- a/findDMR/test-data/MetaTable.csv Thu May 11 11:26:02 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -"channel_count","characteristics_ch1","contact_address","contact_city","contact_country","contact_department","contact_institute","contact_name","contact_zip.postal_code","data_processing","data_row_count","description","extract_protocol_ch1","geo_accession","hyb_protocol","label_ch1","label_protocol_ch1","last_update_date","molecule_ch1","organism_ch1","platform_id","scan_protocol","series_id","source_name_ch1","status","submission_date","supplementary_file","taxid_ch1","title","type" -"1","sample type: melanoma cell line","Barngatan 2B","Lund","Sweden","Dept of Oncology","Lund University","Martin,,Lauss","22185","Raw intensities for methylated (M) and unmethylated (U) signal were extracted from Illumina’s GenomeStudio. Beta-values were calculated as M/(M+U). A total of 496 missing values (melanomas) were imputed using k-nearest neighbor imputation (k=10). For each sample we performed a peak-based correction of Illumina I and II chemical assays. For both assays we smoothed the beta values (Epanechnikov smoothing kernel) to estimate unmethylated and methylated peaks, respectively; and the unmethylated peak was moved to 0 and the methylated peak to 1 using linear scaling, with beta-values in between stretched accordingly. Beta-values below 0 were set back to 0 and values above 1 were set to 1.","485577","melanoma cell line","Genomic DNA was extracted from the biopsies using QIAamp DNA Mini Kit (Qiagen). A total of 500 ng of DNA were used for bisulfite treatment, using the EZ DNA Methylation Kit (Zymo). We hybridized 200 ng in 4 μl to the Infinium Human Methylation450 BeadChip array.","GSM1247787","Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol","Cy5 and Cy3","Standard Illumina Protocol","May 17 2015","genomic DNA","Homo sapiens","GPL13534","Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting","GSE51547","SKMEL3","Public on May 17 2015","Oct 22 2013","NONE","9606","genomic DNA from Sample SKMEL3","genomic" |
| b |
| diff -r 24ac6f93cc3e -r 083895dbc289 findDMR/test-data/input.csv --- a/findDMR/test-data/input.csv Thu May 11 11:26:02 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -ID,Phenotype -GSM1247787,melanoma -GSM1247784,melanoma -GSM1247733,healthy |
| b |
| diff -r 24ac6f93cc3e -r 083895dbc289 findDMR/tool_dependencies.xml --- a/findDMR/tool_dependencies.xml Thu May 11 11:26:02 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="450kdependency" version="0.0.1"> - # TODO: - <repository changeset_revision="6ab5f9bf0d30" name="450kdependency" owner="testtool" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="R" version="3.2.1"> - <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |