Mercurial > repos > sblanck > smagexp
changeset 13:7c49b4ec8cff draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit f0af01c5d808f31a7190449069ccb197807603af-dirty
| author | sblanck |
|---|---|
| date | Thu, 11 May 2017 11:08:05 -0400 |
| parents | 2da91c541ae4 |
| children | e5a94bc69bd6 |
| files | Analyse.R |
| diffstat | 1 files changed, 4 insertions(+), 23 deletions(-) [+] |
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--- a/Analyse.R Thu May 11 10:55:07 2017 -0400 +++ b/Analyse.R Thu May 11 11:08:05 2017 -0400 @@ -42,7 +42,6 @@ #loading libraries suppressPackageStartupMessages(require(GEOquery)) - suppressPackageStartupMessages(require(Biobase)) suppressPackageStartupMessages(require(GEOquery)) suppressPackageStartupMessages(require(GEOmetadb)) @@ -65,8 +64,6 @@ result.template=opt$htmltemplate tooldirectory=opt$tooldirectory -#file.copy(targetFile,"./targetFile.txt") - targets <- read.table(targetFile,sep="\t",stringsAsFactors=FALSE) #condition1_tmp <- strsplit(condition1,",") @@ -78,40 +75,26 @@ conditions=c(condition1,condition2) -#nbresult=1000 dir.create(result.path, showWarnings = TRUE, recursive = FALSE) eset=eset[,which(rownames(eset@phenoData@data) %in% conditions)] -rownames(eset@phenoData@data) -which(rownames(eset@phenoData@data) %in% conditions) -#condition1Name=make.names(condition1Name) -#condition2Name=make.names(condition2Name) -#condition1Name=gsub("_","",condition1Name) -#condition2Name=gsub("_","",condition2Name) -#condition1Name -#condition2Name - eset@phenoData@data$source_name_ch1="" eset@phenoData@data$source_name_ch1[which(rownames(eset@phenoData@data) %in% condition1)]=condition1Name eset@phenoData@data$source_name_ch1[which(rownames(eset@phenoData@data) %in% condition2)]=condition2Name -#condition1Name -#condition2Name condNames=paste0("G",as.numeric(as.character(pData(eset)["source_name_ch1"][,1])!=condition1Name)) -#condNames=make.names(targets[,2]) -#condNames=gsub("_","",condNames) + f <- as.factor(condNames) -#eset$description <- factors + design <- model.matrix(~ 0+f) colnames(design) <- levels(f) -#colnames(design) + fit <- lmFit(eset, design) -#cont.matrix <- makeContrasts(C1=paste0(condition1Name,"-",condition2Name), levels=design) cont.matrix <- makeContrasts(G0-G1, levels=design) -#cont.matrix + fit2 <- contrasts.fit(fit, cont.matrix) fit2 <- eBayes(fit2) @@ -122,7 +105,6 @@ gpl <- annotation(eset) if (substr(x = gpl,1,3)!="GPL"){ #if the annotation info does not start with "GPL" we retrieve the corresponding GPL annotation - print(getwd()) mapping=read.csv(paste0(tooldirectory,"/gplToBioc.csv"),stringsAsFactors=FALSE) gpl=mapping[which(mapping$bioc_package==annotation(eset)),]$gpl gpl=gpl[1] @@ -181,7 +163,6 @@ dev.off() file.copy(histopvalue,result.path) -#write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions) saveConditions=c(condition1Name,condition2Name) save(eset,saveConditions,file=result_export_eset) write.table(x=tT[,-1],file=result.tabular,quote=FALSE,row.names=FALSE,col.names=TRUE,sep="\t")