| Previous changeset 4:49c36c54e0cf (2020-01-03) Next changeset 6:ec75de7f1e08 (2023-12-11) |
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Commit message:
Uploaded |
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modified:
Intchecks/Script_intensity_check.R Intchecks/xml_intensity_check.xml |
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| diff -r 49c36c54e0cf -r a31f3f802b2b Intchecks/Script_intensity_check.R --- a/Intchecks/Script_intensity_check.R Fri Jan 03 11:09:05 2020 -0500 +++ b/Intchecks/Script_intensity_check.R Wed Jan 22 09:34:08 2020 -0500 |
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| @@ -69,12 +69,19 @@ table.check <- match3(DM, SM, VM) check.err(table.check) - + # Transposing the dataMatrix rownames(DM) <- DM[,1] var_names <- DM[,1] DM <- DM[,-1] DM <- data.frame(t(DM)) - + + # Re-ordering the dataMatrix to match the sampleMetadata file order + DM <- merge(x=cbind(1:nrow(SM),SM), y=DM, by.x=2, by.y=0) + DM <- DM[order(DM[,2]),] + rownames(DM) <- DM[,1] + DM <- DM[,-c(1:(ncol(SM)+1))] + + stat.list <- strsplit(chosen.stat,",")[[1]] @@ -103,13 +110,13 @@ classnames <- levels(c_class) if((nb_class < 2)&&(test.fold=="Yes")){ - err.1class <- c("\n The column",class.col, "contains only one class, fold calculation could not be executed \n") + err.1class <- c("\n The column",class.col, "contains only one class, fold calculation could not be executed. \n") cat(err.1class) } if((nb_class > (nrow(SM))/3)&&(method == "each_class")){ class.err <- c("\n There are too many classes, think about reducing the number of classes and excluding those - with few samples \n") + with few samples. \n") cat(class.err) } @@ -139,6 +146,37 @@ # Statistics ------------------------------------------------------------------------------------------------ + # Check whether the dataMatrix contains non-numeric values + if(!(is.numeric(as.matrix(DM)))){ + # findchar definition + findchar <- function(myval){ + if(is.na(myval)){ + return("ok") + }else{ + mytest <- as.character(myval) + if(is.na(as.numeric(mytest[1]))){ + return("char") + }else{ + return("ok") + } + } + } + # findchar application + chardiag <- suppressWarnings(apply(DM,2,vapply,findchar,"character")) + charlist <- which(chardiag == "char") + err.stock <- paste("\n- - - - - - - - -\nYour dataMatrix contains", + length(charlist), + "non-numeric value(s). To help you check your data, please find below a short overview:\n") + charover <- 1 + while((length(err.stock)<10)&(length(err.stock)<(length(charlist)+1))){ + charex <- paste("variable",colnames(DM)[ceiling(charlist[charover]/nrow(DM))], + "- sample",rownames(DM)[charlist[charover]-floor(charlist[charover]/nrow(DM))*nrow(DM)], + "~> value:",as.matrix(DM)[charlist[charover]],"\n") + err.stock <- c(err.stock,charex) + charover <- charover + 1 + } + stop(c(err.stock,"The dataMatrix file is supposed to contain only numeric values.\n- - - - - - - - -\n")) + } ### Initialization |
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| diff -r 49c36c54e0cf -r a31f3f802b2b Intchecks/xml_intensity_check.xml --- a/Intchecks/xml_intensity_check.xml Fri Jan 03 11:09:05 2020 -0500 +++ b/Intchecks/xml_intensity_check.xml Wed Jan 22 09:34:08 2020 -0500 |
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| @@ -129,6 +129,7 @@ </outputs> + <help> |