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R/oneChannelGUI.R
In oneChannelGUI: A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
#This function is used to start oneChannelGUI
#contains oneChannelGUI initialize.extAffylmGUI
# affylmGUI affylmGUI
"oneChannelGUI" <- function(){
#require(affylmGUI) || stop("\nneed package: affylmGUI\n")
# library(affylmGUI)
Try(if(.Platform$OS.type=="windows"){
initialize.extAffylmGUI()
tt <- ""
assign("unfilteredData.location", tt, affylmGUIenvironment)
assign("whichArrayPlatform", tt,affylmGUIenvironment)#this will be set by the loaded platform 3'IVT, exons, illumina, AB1700
assign("geoPlatform", tt, env=affylmGUIenvironment)
assign("metaData.Available",FALSE,affylmGUIenvironment)
assign("metaData",tt,affylmGUIenvironment)
assign("exprConsoleLibs.Available",FALSE,affylmGUIenvironment)
assign("exprConsoleLibs", tt ,affylmGUIenvironment)#locate here the library files as a list of data.frames
#gathering affy libs and apt tools folders
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(javaDir <- myinfo[which(myinfo[,1]=="javaDir"),2])
if(is.na(javaDir)){
Try(javaDir <- tt)
Try(assign("javaDir",javaDir,affylmGUIenvironment))
Try(assign("javaDir.Available",FALSE,affylmGUIenvironment))
} else if(javaDir == ""){
assign("javaDir", javaDir, affylmGUIenvironment)#directory where java is located
assign("javaDir.Available",FALSE,affylmGUIenvironment)
} else if(javaDir != ""){
assign("javaDir", javaDir, affylmGUIenvironment)#directory where java is located
assign("javaDir.Available",TRUE,affylmGUIenvironment)
}
Try(binDir <- myinfo[which(myinfo[,1]=="binDir"),2])
if(is.na(binDir)) {
Try(binDir <- tt)
Try(assign("binDir",binDir,affylmGUIenvironment))
Try(assign("binDir.Available",FALSE,affylmGUIenvironment))
} else if(binDir == ""){
assign("binDir", binDir, affylmGUIenvironment)#bin dir
assign("binDir.Available",FALSE,affylmGUIenvironment)
} else if(binDir != ""){
assign("binDir", binDir, affylmGUIenvironment)#bin dir
assign("binDir.Available",TRUE,affylmGUIenvironment)
}
Try(libDirLocation <- myinfo[which(myinfo[,1]=="libDirLocation"),2])
if(is.na(libDirLocation)) {
Try(libDirLocation <- tt)
Try(assign("libDirLocation",libDirLocation,affylmGUIenvironment))
Try(assign("libDir.Available",FALSE,affylmGUIenvironment))
}else if(libDirLocation == ""){
assign("libDirLocation", libDirLocation, affylmGUIenvironment)#directory where exon data are located
assign("libDirLocation.Available",FALSE,affylmGUIenvironment)
}else if(libDirLocation != ""){
assign("libDirLocation", libDirLocation, affylmGUIenvironment)#directory where exon data are located
assign("libDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(meVDirLocation <- myinfo[which(myinfo[,1]=="meVDirLocation"),2])
if(is.na(meVDirLocation)){
Try(meVDirLocation <- tt)
Try(assign("meVDirLocation",meVDirLocation,affylmGUIenvironment))
Try(assign("meVDirLocation.Available",FALSE,affylmGUIenvironment))
} else if(meVDirLocation == ""){
assign("meVDirLocation", meVDirLocation, affylmGUIenvironment)#directory where meV program is located
assign("meVDirLocation.Available",FALSE,affylmGUIenvironment)
} else if(meVDirLocation != ""){
assign("meVDirLocation", meVDirLocation, affylmGUIenvironment)#directory where meV program is located
assign("meVDirLocation.Available",TRUE,affylmGUIenvironment)
}
#needed for Affymetrix gene arrays
Try(assign("geneLibsInfo", tt ,affylmGUIenvironment))
#Try(perlDirLocation <- myinfo[which(myinfo[,1]=="perlDirLocation"),2]) #loacation of per ngs scripts
Try(perlDirLocation <- paste(path.package("oneChannelGUI", quiet = F),"/perl_scripts/", sep=""))
#Try(if(is.na(perlDirLocation)) perlDirLocation <- tt)
Try(assign("perlDirLocation",perlDirLocation,affylmGUIenvironment))
Try(assign("perlDirLocation.Available",TRUE,affylmGUIenvironment))
Try(pythonDirLocation <- paste(path.package("oneChannelGUI", quiet = F),"/inst/python_scripts/", sep=""))
Try(assign("pythonDirLocation",pythonDirLocation,affylmGUIenvironment))
Try(assign("pythonDirLocation.Available",TRUE,affylmGUIenvironment))
# if(perlDirLocation != ""){
# assign("perlDirLocation", perlDirLocation, affylmGUIenvironment)#directory where ngs perl scripts are located
# assign("perlDirLocation.Available",TRUE,affylmGUIenvironment)
# }
Try(tophatDirLocation <- myinfo[which(myinfo[,1]=="tophatDirLocation"),2]) #loacation of tophat
if(is.na(tophatDirLocation)) {
Try(tophatDirLocation <- tt)
Try(assign("tophatDirLocation",tophatDirLocation,affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(tophatDirLocation=="") {
Try(assign("tophatDirLocation",tt,affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (tophatDirLocation != ""){
assign("tophatDirLocation", tophatDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("tophatDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(cuffDirLocation <- myinfo[which(myinfo[,1]=="cuffDirLocation"),2]) #loacation of cuff
if(is.na(cuffDirLocation)) {
Try(cuffDirLocation <- tt)
Try(assign("cuffDirLocation",cuffDirLocation,affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(cuffDirLocation=="") {
Try(assign("cuffDirLocation",tt,affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (cuffDirLocation != ""){
assign("cuffDirLocation", cuffDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("cuffDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(samtoolsDirLocation <- myinfo[which(myinfo[,1]=="samtoolsDirLocation"),2]) #loacation of tophat
if(is.na(samtoolsDirLocation)) {
Try(samtoolsDirLocation <- tt)
Try(assign("samtoolsDirLocation",samtoolsDirLocation,affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(samtoolsDirLocation=="") {
Try(assign("samtoolsDirLocation",tt,affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (samtoolsDirLocation != ""){
assign("samtoolsDirLocation", samtoolsDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("samtoolsDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(fastqcDirLocation <- myinfo[which(myinfo[,1]=="fastqcDirLocation"),2]) #loacation of tophat
if(is.na(fastqcDirLocation)) {
Try(fastqcDirLocation <- tt)
Try(assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment))
Try(assign("fastqcDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(fastqcDirLocation=="") {
Try(assign("fastqcDirLocation",tt,affylmGUIenvironment))
Try(assign("fastqcDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (fastqcDirLocation != ""){
assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("fastqcDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(bowtieDirLocation <- myinfo[which(myinfo[,1]=="bowtieDirLocation"),2]) #loacation of bowtie
if(is.na(bowtieDirLocation)) {
Try(bowtieDirLocation <- tt)
Try(assign("bowtieDirLocation",bowtieDirLocation,affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(bowtieDirLocation=="") {
Try(assign("bowtieDirLocation",tt,affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (bowtieDirLocation != ""){
assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment)#directory where bowtie is located
assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(shrimpDirLocation <- myinfo[which(myinfo[,1]=="shrimpDirLocation"),2]) #loacation of shrimp
if(is.na(shrimpDirLocation)) {
Try(shrimpDirLocation <- tt)
Try(assign("shrimpDirLocation",shrimpDirLocation,affylmGUIenvironment))
Try(assign("shrimpDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(shrimpDirLocation=="") {
Try(assign("shrimpDirLocation",tt,affylmGUIenvironment))
Try(assign("shrimpDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (shrimpDirLocation != ""){
assign("shrimpDirLocation", shrimpDirLocation, affylmGUIenvironment)#directory where shrimp is located
assign("shrimpDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(bowtieRefs <- myinfo[which(myinfo[,1]=="bowtieRefs"),2])
Try(bowtieRefs <- as.vector(unlist(strsplit(bowtieRefs, ","))))
Try(names(bowtieRefs) <- c("hg19","mm9","rn4"))
Try(assign("bowtieRefs",bowtieRefs,affylmGUIenvironment))
assign("libDir", libDirLocation ,affylmGUIenvironment)#locate here the library files as a list of data.frames
assign("whichLib", tt ,affylmGUIenvironment)#remember the type of exon library loaded
assign("miRname", tt ,affylmGUIenvironment)
assign("miRname.available", FALSE,affylmGUIenvironment)
Try(aptDir <- myinfo[which(myinfo[,1]=="aptDir"),2])
Try(if(is.na(aptDir)) aptDir <- tt)
if(aptDir != ""){
assign("aptDir.Available",TRUE,affylmGUIenvironment)
assign("aptDir", aptDir ,affylmGUIenvironment)
} else{
assign("aptDir.Available",FALSE,affylmGUIenvironment)
assign("aptDir", tt ,affylmGUIenvironment)
}
assign("cosie.Available", FALSE ,affylmGUIenvironment)
assign("EG2probeset.available", FALSE, affylmGUIenvironment)
assign("EG2probeset", tt, affylmGUIenvironment)
assign("exonAffyData.Available",FALSE,affylmGUIenvironment)
assign("exonAffyData", tt ,affylmGUIenvironment)
assign("dabg.Available" , FALSE, affylmGUIenvironment)
assign("dabg.p" , tt, affylmGUIenvironment)
assign("midas.p" , tt, affylmGUIenvironment)
assign("midas.p.Available" , FALSE, affylmGUIenvironment)
assign("spliceIndexData.Available",FALSE,affylmGUIenvironment)
assign("spliceIndexData", tt ,affylmGUIenvironment)
assign("AltSplRP.e.p" , tt, affylmGUIenvironment)
assign("AltSplRP.e.Available" , FALSE, affylmGUIenvironment)
assign("AltSplRP.g" , tt, affylmGUIenvironment)
assign("AltSplRP.g.Available" , FALSE, affylmGUIenvironment)
assign("mapping2ensembl" , tt, affylmGUIenvironment)
assign("mapping2ensembl.Available" , FALSE, affylmGUIenvironment)
assign("exonsSpecific2as" , tt, affylmGUIenvironment)
assign("exonsSpecific2as.Available" , FALSE, affylmGUIenvironment)
Try(assign("fitExon",tt,affylmGUIenvironment))
Try(assign("LinearModelFitExon.Available",FALSE,affylmGUIenvironment))
Try(assign("AltSplLimma" , tt, affylmGUIenvironment))
Try(assign("AltSplLimma.Available" , FALSE, affylmGUIenvironment))
Try(assign("intronicBg.available", TRUE,affylmGUIenvironment))
Try(assign("intronicBg", tt,affylmGUIenvironment))
assign("maSigProSigs.Available",FALSE,affylmGUIenvironment)
assign("Pset.Available",FALSE,affylmGUIenvironment)
assign("MLdesign.Available",FALSE,affylmGUIenvironment)
assign("MLdesign", tt ,affylmGUIenvironment)
assign("trainAffyData.available", FALSE, env=affylmGUIenvironment)
assign("testAffyData.available", FALSE, env=affylmGUIenvironment)
#NGS data
assign("NGS", tt ,affylmGUIenvironment)
assign("NGS.Available", FALSE, env=affylmGUIenvironment)
assign("NGSconversion.available", FALSE, env=affylmGUIenvironment)
assign("Genominator.Available", FALSE, env=affylmGUIenvironment)
assign("GenominatorDB",tt,affylmGUIenvironment)
assign("NGSscaling.Available", FALSE, env=affylmGUIenvironment)
assign("NGSprimaryMapping", tt ,affylmGUIenvironment) #used to know the type of data format to be loaded
assign("NGSprimaryMapping.Available", FALSE, env=affylmGUIenvironment)
#this should be updated also in the NewLimmafile because if a new project is loaded these variables
#are not initialized it would be better to make them in a function
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","maSIgProData" ,text="maSigPro results",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","maSIgProData","maSIgProData.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","PLM" ,text="PLM data",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","PLM","PLM.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","ExonArrays" ,text="Normalized Exon data from Expression Console",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","ExonArrays","ExonArrays.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AptDabg" ,text="APT DABG",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AptDabg","AptDabg.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AptMidas" ,text="APT MiDAS",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AptMidas","AptMidas.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","spliceIndex" ,text="Splice Index",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","spliceIndex","spliceIndex.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AltSplRP" ,text="Alternative Splicing by RP",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AltSplRP","AltSplRP.e.Status" ,text="Not Available at exon level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AltSplRP","AltSplRP.g.Status" ,text="Not Available at gene level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","metaData" ,text="Meta analysis",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","metaData","metaData.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","classification" ,text="Classification Params",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","classification","classification.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","LinearModelFitExon" ,text="Limma exon-level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","LinearModelFitExon","LinearModelFitExon.Status",text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","NGS" ,text="NGS data",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","NGS","NGS.Status",text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
#remember the previous part should be updated also down in the else in this function and
# in the NewLimmaFile and OpenLimmaFile function selection affy/exon/large/geo
assign("Pset" , tt, affylmGUIenvironment)
#Try(changes())
} else {
affylmGUI()
initialize.extAffylmGUI()
tt <- ""
assign("unfilteredData.location", tt, affylmGUIenvironment)
assign("whichArrayPlatform", tt,affylmGUIenvironment)#this will be set by the loaded platform 3'IVT, exons, illumina, AB1700
assign("geoPlatform", tt, env=affylmGUIenvironment)
assign("metaData.Available",FALSE,affylmGUIenvironment)
assign("metaData",tt,affylmGUIenvironment)
assign("exprConsoleLibs.Available",FALSE,affylmGUIenvironment)
assign("exprConsoleLibs", tt ,affylmGUIenvironment)#locate here the library files as a list of data.frames
#gathering affy libs and apt tools folders
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(javaDir <- myinfo[which(myinfo[,1]=="javaDir"),2])
if(is.na(javaDir)){
Try(javaDir <- tt)
Try(assign("javaDir",javaDir,affylmGUIenvironment))
Try(assign("javaDir.Available",FALSE,affylmGUIenvironment))
} else if(javaDir == ""){
assign("javaDir", javaDir, affylmGUIenvironment)#directory where java is located
assign("javaDir.Available",FALSE,affylmGUIenvironment)
} else if(javaDir != ""){
assign("javaDir", javaDir, affylmGUIenvironment)#directory where java is located
assign("javaDir.Available",TRUE,affylmGUIenvironment)
}
Try(binDir <- myinfo[which(myinfo[,1]=="binDir"),2])
if(is.na(binDir)) {
Try(binDir <- tt)
Try(assign("binDir",binDir,affylmGUIenvironment))
Try(assign("binDir.Available",FALSE,affylmGUIenvironment))
} else if(binDir == ""){
assign("binDir", binDir, affylmGUIenvironment)#bin dir
assign("binDir.Available",FALSE,affylmGUIenvironment)
} else if(binDir != ""){
assign("binDir", binDir, affylmGUIenvironment)#bin dir
assign("binDir.Available",TRUE,affylmGUIenvironment)
}
Try(libDirLocation <- myinfo[which(myinfo[,1]=="libDirLocation"),2])
if(is.na(libDirLocation)) {
Try(libDirLocation <- tt)
Try(assign("libDirLocation",libDirLocation,affylmGUIenvironment))
Try(assign("libDir.Available",FALSE,affylmGUIenvironment))
}else if(libDirLocation == ""){
assign("libDirLocation", libDirLocation, affylmGUIenvironment)#directory where exon data are located
assign("libDirLocation.Available",FALSE,affylmGUIenvironment)
}else if(libDirLocation != ""){
assign("libDirLocation", libDirLocation, affylmGUIenvironment)#directory where exon data are located
assign("libDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(meVDirLocation <- myinfo[which(myinfo[,1]=="meVDirLocation"),2])
if(is.na(meVDirLocation)){
Try(meVDirLocation <- tt)
Try(assign("meVDirLocation",meVDirLocation,affylmGUIenvironment))
Try(assign("meVDirLocation.Available",FALSE,affylmGUIenvironment))
} else if(meVDirLocation == ""){
assign("meVDirLocation", meVDirLocation, affylmGUIenvironment)#directory where meV program is located
assign("meVDirLocation.Available",FALSE,affylmGUIenvironment)
} else if(meVDirLocation != ""){
assign("meVDirLocation", meVDirLocation, affylmGUIenvironment)#directory where meV program is located
assign("meVDirLocation.Available",TRUE,affylmGUIenvironment)
}
#needed for Affymetrix gene arrays
Try(assign("geneLibsInfo", tt ,affylmGUIenvironment))
#Try(perlDirLocation <- myinfo[which(myinfo[,1]=="perlDirLocation"),2]) #loacation of per ngs scripts
#Try(if(is.na(perlDirLocation)) perlDirLocation <- tt)
Try(perlDirLocation <- paste(path.package("oneChannelGUI", quiet = F),"/perl_scripts/", sep=""))
Try(assign("perlDirLocation",perlDirLocation,affylmGUIenvironment))
Try(assign("perlDirLocation.Available",TRUE,affylmGUIenvironment))
Try(pythonDirLocation <- paste(path.package("oneChannelGUI", quiet = F),"/inst/python_scripts/", sep=""))
Try(assign("pythonDirLocation",pythonDirLocation,affylmGUIenvironment))
Try(assign("pythonDirLocation.Available",TRUE,affylmGUIenvironment))
# if(perlDirLocation != ""){
# assign("perlDirLocation", perlDirLocation, affylmGUIenvironment)#directory where ngs perl scripts are located
# assign("perlDirLocation.Available",TRUE,affylmGUIenvironment)
# }
Try(tophatDirLocation <- myinfo[which(myinfo[,1]=="tophatDirLocation"),2]) #loacation of tophat
if(is.na(tophatDirLocation)) {
Try(tophatDirLocation <- tt)
Try(assign("tophatDirLocation",tophatDirLocation,affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(tophatDirLocation=="") {
Try(assign("tophatDirLocation",tt,affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (tophatDirLocation != ""){
assign("tophatDirLocation", tophatDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("tophatDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(cuffDirLocation <- myinfo[which(myinfo[,1]=="cuffDirLocation"),2]) #loacation of cuff
if(is.na(cuffDirLocation)) {
Try(cuffDirLocation <- tt)
Try(assign("cuffDirLocation",cuffDirLocation,affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(cuffDirLocation=="") {
Try(assign("cuffDirLocation",tt,affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (cuffDirLocation != ""){
assign("cuffDirLocation", cuffDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("cuffDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(samtoolsDirLocation <- myinfo[which(myinfo[,1]=="samtoolsDirLocation"),2]) #loacation of tophat
if(is.na(samtoolsDirLocation)) {
Try(samtoolsDirLocation <- tt)
Try(assign("samtoolsDirLocation",samtoolsDirLocation,affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(samtoolsDirLocation=="") {
Try(assign("samtoolsDirLocation",tt,affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (samtoolsDirLocation != ""){
assign("samtoolsDirLocation", samtoolsDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("samtoolsDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(fastqcDirLocation <- myinfo[which(myinfo[,1]=="fastqcDirLocation"),2]) #loacation of tophat
if(is.na(fastqcDirLocation)) {
Try(fastqcDirLocation <- tt)
Try(assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment))
Try(assign("fastqcDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(fastqcDirLocation=="") {
Try(assign("fastqcDirLocation",tt,affylmGUIenvironment))
Try(assign("fastqcDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (fastqcDirLocation != ""){
assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("fastqcDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(bowtieDirLocation <- myinfo[which(myinfo[,1]=="bowtieDirLocation"),2]) #loacation of bowtie
if(is.na(bowtieDirLocation)) {
Try(bowtieDirLocation <- tt)
Try(assign("bowtieDirLocation",bowtieDirLocation,affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(bowtieDirLocation=="") {
Try(assign("bowtieDirLocation",tt,affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (bowtieDirLocation != ""){
assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment)#directory where bowtie is located
assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(shrimpDirLocation <- myinfo[which(myinfo[,1]=="shrimpDirLocation"),2]) #loacation of shrimp
if(is.na(shrimpDirLocation)) {
Try(shrimpDirLocation <- tt)
Try(assign("shrimpDirLocation",shrimpDirLocation,affylmGUIenvironment))
Try(assign("shrimpDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(shrimpDirLocation=="") {
Try(assign("shrimpDirLocation",tt,affylmGUIenvironment))
Try(assign("shrimpDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (shrimpDirLocation != ""){
assign("shrimpDirLocation", shrimpDirLocation, affylmGUIenvironment)#directory where shrimp is located
assign("shrimpDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(bowtieRefs <- myinfo[which(myinfo[,1]=="bowtieRefs"),2])
Try(bowtieRefs <- as.vector(unlist(strsplit(bowtieRefs, ","))))
Try(names(bowtieRefs) <- c("hg19","mm9","rn4"))
Try(assign("bowtieRefs",bowtieRefs,affylmGUIenvironment))
assign("libDir", libDirLocation ,affylmGUIenvironment)#locate here the library files as a list of data.frames
assign("whichLib", tt ,affylmGUIenvironment)#remember the type of exon library loaded
assign("miRname", tt ,affylmGUIenvironment)
assign("miRname.available", FALSE,affylmGUIenvironment)
Try(aptDir <- myinfo[which(myinfo[,1]=="aptDir"),2])
Try(if(is.na(aptDir)) aptDir <- tt)
if(aptDir != ""){
assign("aptDir.Available",TRUE,affylmGUIenvironment)
assign("aptDir", aptDir ,affylmGUIenvironment)
} else{
assign("aptDir.Available",FALSE,affylmGUIenvironment)
assign("aptDir", tt ,affylmGUIenvironment)
}
assign("cosie.Available", FALSE ,affylmGUIenvironment)
assign("EG2probeset.available", FALSE, affylmGUIenvironment)
assign("EG2probeset", tt, affylmGUIenvironment)
assign("exonAffyData.Available",FALSE,affylmGUIenvironment)
assign("exonAffyData", tt ,affylmGUIenvironment)
assign("dabg.Available" , FALSE, affylmGUIenvironment)
assign("dabg.p" , tt, affylmGUIenvironment)
assign("midas.p" , tt, affylmGUIenvironment)
assign("midas.p.Available" , FALSE, affylmGUIenvironment)
assign("spliceIndexData.Available",FALSE,affylmGUIenvironment)
assign("spliceIndexData", tt ,affylmGUIenvironment)
assign("AltSplRP.e.p" , tt, affylmGUIenvironment)
assign("AltSplRP.e.Available" , FALSE, affylmGUIenvironment)
assign("AltSplRP.g" , tt, affylmGUIenvironment)
assign("AltSplRP.g.Available" , FALSE, affylmGUIenvironment)
assign("mapping2ensembl" , tt, affylmGUIenvironment)
assign("mapping2ensembl.Available" , FALSE, affylmGUIenvironment)
assign("exonsSpecific2as" , tt, affylmGUIenvironment)
assign("exonsSpecific2as.Available" , FALSE, affylmGUIenvironment)
Try(assign("fitExon",tt,affylmGUIenvironment))
Try(assign("LinearModelFitExon.Available",FALSE,affylmGUIenvironment))
Try(assign("AltSplLimma" , tt, affylmGUIenvironment))
Try(assign("AltSplLimma.Available" , FALSE, affylmGUIenvironment))
Try(assign("intronicBg.available", TRUE,affylmGUIenvironment))
Try(assign("intronicBg", tt,affylmGUIenvironment))
assign("maSigProSigs.Available",FALSE,affylmGUIenvironment)
assign("Pset.Available",FALSE,affylmGUIenvironment)
assign("MLdesign.Available",FALSE,affylmGUIenvironment)
assign("MLdesign", tt ,affylmGUIenvironment)
assign("trainAffyData.available", FALSE, env=affylmGUIenvironment)
assign("testAffyData.available", FALSE, env=affylmGUIenvironment)
#NGS data
assign("NGS", tt ,affylmGUIenvironment)
assign("NGS.Available", FALSE, env=affylmGUIenvironment)
assign("NGSconversion.available", FALSE, env=affylmGUIenvironment)
assign("Genominator.Available", FALSE, env=affylmGUIenvironment)
assign("GenominatorDB",tt,affylmGUIenvironment)
assign("NGSscaling.Available", FALSE, env=affylmGUIenvironment)
assign("NGSprimaryMapping", tt ,affylmGUIenvironment)
assign("NGSprimaryMapping.Available", FALSE, env=affylmGUIenvironment)
#this should be updated also in the NewLimmafile because if a new project is loaded these variables
#are not initialized it would be better to make them in a function
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","maSIgProData" ,text="maSigPro results",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","maSIgProData","maSIgProData.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","PLM" ,text="PLM data",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","PLM","PLM.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","ExonArrays" ,text="Normalized Exon data from Expression Console",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","ExonArrays","ExonArrays.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AptDabg" ,text="APT DABG",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AptDabg","AptDabg.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AptMidas" ,text="APT MiDAS",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AptMidas","AptMidas.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","spliceIndex" ,text="Splice Index",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","spliceIndex","spliceIndex.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AltSplRP" ,text="Alternative Splicing by RP",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AltSplRP","AltSplRP.e.Status" ,text="Not Available at exon level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AltSplRP","AltSplRP.g.Status" ,text="Not Available at gene level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","metaData" ,text="Meta analysis",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","metaData","metaData.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","classification" ,text="Classification Params",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","classification","classification.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","LinearModelFitExon" ,text="Limma exon-level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","LinearModelFitExon","LinearModelFitExon.Status",text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
#NGS
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","NGS" ,text="NGS data",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","NGS","NGS.Status",text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
#remember the previous part should be updated also down in the else in this function and
# in the NewLimmaFile and OpenLimmaFile function selection affy/exon/large/geo
assign("Pset" , tt, affylmGUIenvironment)
#Try(changes())
})
}
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#This function is used to start oneChannelGUI
#contains oneChannelGUI initialize.extAffylmGUI
# affylmGUI affylmGUI
"oneChannelGUI" <- function(){
#require(affylmGUI) || stop("\nneed package: affylmGUI\n")
# library(affylmGUI)
Try(if(.Platform$OS.type=="windows"){
initialize.extAffylmGUI()
tt <- ""
assign("unfilteredData.location", tt, affylmGUIenvironment)
assign("whichArrayPlatform", tt,affylmGUIenvironment)#this will be set by the loaded platform 3'IVT, exons, illumina, AB1700
assign("geoPlatform", tt, env=affylmGUIenvironment)
assign("metaData.Available",FALSE,affylmGUIenvironment)
assign("metaData",tt,affylmGUIenvironment)
assign("exprConsoleLibs.Available",FALSE,affylmGUIenvironment)
assign("exprConsoleLibs", tt ,affylmGUIenvironment)#locate here the library files as a list of data.frames
#gathering affy libs and apt tools folders
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(javaDir <- myinfo[which(myinfo[,1]=="javaDir"),2])
if(is.na(javaDir)){
Try(javaDir <- tt)
Try(assign("javaDir",javaDir,affylmGUIenvironment))
Try(assign("javaDir.Available",FALSE,affylmGUIenvironment))
} else if(javaDir == ""){
assign("javaDir", javaDir, affylmGUIenvironment)#directory where java is located
assign("javaDir.Available",FALSE,affylmGUIenvironment)
} else if(javaDir != ""){
assign("javaDir", javaDir, affylmGUIenvironment)#directory where java is located
assign("javaDir.Available",TRUE,affylmGUIenvironment)
}
Try(binDir <- myinfo[which(myinfo[,1]=="binDir"),2])
if(is.na(binDir)) {
Try(binDir <- tt)
Try(assign("binDir",binDir,affylmGUIenvironment))
Try(assign("binDir.Available",FALSE,affylmGUIenvironment))
} else if(binDir == ""){
assign("binDir", binDir, affylmGUIenvironment)#bin dir
assign("binDir.Available",FALSE,affylmGUIenvironment)
} else if(binDir != ""){
assign("binDir", binDir, affylmGUIenvironment)#bin dir
assign("binDir.Available",TRUE,affylmGUIenvironment)
}
Try(libDirLocation <- myinfo[which(myinfo[,1]=="libDirLocation"),2])
if(is.na(libDirLocation)) {
Try(libDirLocation <- tt)
Try(assign("libDirLocation",libDirLocation,affylmGUIenvironment))
Try(assign("libDir.Available",FALSE,affylmGUIenvironment))
}else if(libDirLocation == ""){
assign("libDirLocation", libDirLocation, affylmGUIenvironment)#directory where exon data are located
assign("libDirLocation.Available",FALSE,affylmGUIenvironment)
}else if(libDirLocation != ""){
assign("libDirLocation", libDirLocation, affylmGUIenvironment)#directory where exon data are located
assign("libDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(meVDirLocation <- myinfo[which(myinfo[,1]=="meVDirLocation"),2])
if(is.na(meVDirLocation)){
Try(meVDirLocation <- tt)
Try(assign("meVDirLocation",meVDirLocation,affylmGUIenvironment))
Try(assign("meVDirLocation.Available",FALSE,affylmGUIenvironment))
} else if(meVDirLocation == ""){
assign("meVDirLocation", meVDirLocation, affylmGUIenvironment)#directory where meV program is located
assign("meVDirLocation.Available",FALSE,affylmGUIenvironment)
} else if(meVDirLocation != ""){
assign("meVDirLocation", meVDirLocation, affylmGUIenvironment)#directory where meV program is located
assign("meVDirLocation.Available",TRUE,affylmGUIenvironment)
}
#needed for Affymetrix gene arrays
Try(assign("geneLibsInfo", tt ,affylmGUIenvironment))
#Try(perlDirLocation <- myinfo[which(myinfo[,1]=="perlDirLocation"),2]) #loacation of per ngs scripts
Try(perlDirLocation <- paste(path.package("oneChannelGUI", quiet = F),"/perl_scripts/", sep=""))
#Try(if(is.na(perlDirLocation)) perlDirLocation <- tt)
Try(assign("perlDirLocation",perlDirLocation,affylmGUIenvironment))
Try(assign("perlDirLocation.Available",TRUE,affylmGUIenvironment))
Try(pythonDirLocation <- paste(path.package("oneChannelGUI", quiet = F),"/inst/python_scripts/", sep=""))
Try(assign("pythonDirLocation",pythonDirLocation,affylmGUIenvironment))
Try(assign("pythonDirLocation.Available",TRUE,affylmGUIenvironment))
# if(perlDirLocation != ""){
# assign("perlDirLocation", perlDirLocation, affylmGUIenvironment)#directory where ngs perl scripts are located
# assign("perlDirLocation.Available",TRUE,affylmGUIenvironment)
# }
Try(tophatDirLocation <- myinfo[which(myinfo[,1]=="tophatDirLocation"),2]) #loacation of tophat
if(is.na(tophatDirLocation)) {
Try(tophatDirLocation <- tt)
Try(assign("tophatDirLocation",tophatDirLocation,affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(tophatDirLocation=="") {
Try(assign("tophatDirLocation",tt,affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (tophatDirLocation != ""){
assign("tophatDirLocation", tophatDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("tophatDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(cuffDirLocation <- myinfo[which(myinfo[,1]=="cuffDirLocation"),2]) #loacation of cuff
if(is.na(cuffDirLocation)) {
Try(cuffDirLocation <- tt)
Try(assign("cuffDirLocation",cuffDirLocation,affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(cuffDirLocation=="") {
Try(assign("cuffDirLocation",tt,affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (cuffDirLocation != ""){
assign("cuffDirLocation", cuffDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("cuffDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(samtoolsDirLocation <- myinfo[which(myinfo[,1]=="samtoolsDirLocation"),2]) #loacation of tophat
if(is.na(samtoolsDirLocation)) {
Try(samtoolsDirLocation <- tt)
Try(assign("samtoolsDirLocation",samtoolsDirLocation,affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(samtoolsDirLocation=="") {
Try(assign("samtoolsDirLocation",tt,affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (samtoolsDirLocation != ""){
assign("samtoolsDirLocation", samtoolsDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("samtoolsDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(fastqcDirLocation <- myinfo[which(myinfo[,1]=="fastqcDirLocation"),2]) #loacation of tophat
if(is.na(fastqcDirLocation)) {
Try(fastqcDirLocation <- tt)
Try(assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment))
Try(assign("fastqcDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(fastqcDirLocation=="") {
Try(assign("fastqcDirLocation",tt,affylmGUIenvironment))
Try(assign("fastqcDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (fastqcDirLocation != ""){
assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("fastqcDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(bowtieDirLocation <- myinfo[which(myinfo[,1]=="bowtieDirLocation"),2]) #loacation of bowtie
if(is.na(bowtieDirLocation)) {
Try(bowtieDirLocation <- tt)
Try(assign("bowtieDirLocation",bowtieDirLocation,affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(bowtieDirLocation=="") {
Try(assign("bowtieDirLocation",tt,affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (bowtieDirLocation != ""){
assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment)#directory where bowtie is located
assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(shrimpDirLocation <- myinfo[which(myinfo[,1]=="shrimpDirLocation"),2]) #loacation of shrimp
if(is.na(shrimpDirLocation)) {
Try(shrimpDirLocation <- tt)
Try(assign("shrimpDirLocation",shrimpDirLocation,affylmGUIenvironment))
Try(assign("shrimpDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(shrimpDirLocation=="") {
Try(assign("shrimpDirLocation",tt,affylmGUIenvironment))
Try(assign("shrimpDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (shrimpDirLocation != ""){
assign("shrimpDirLocation", shrimpDirLocation, affylmGUIenvironment)#directory where shrimp is located
assign("shrimpDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(bowtieRefs <- myinfo[which(myinfo[,1]=="bowtieRefs"),2])
Try(bowtieRefs <- as.vector(unlist(strsplit(bowtieRefs, ","))))
Try(names(bowtieRefs) <- c("hg19","mm9","rn4"))
Try(assign("bowtieRefs",bowtieRefs,affylmGUIenvironment))
assign("libDir", libDirLocation ,affylmGUIenvironment)#locate here the library files as a list of data.frames
assign("whichLib", tt ,affylmGUIenvironment)#remember the type of exon library loaded
assign("miRname", tt ,affylmGUIenvironment)
assign("miRname.available", FALSE,affylmGUIenvironment)
Try(aptDir <- myinfo[which(myinfo[,1]=="aptDir"),2])
Try(if(is.na(aptDir)) aptDir <- tt)
if(aptDir != ""){
assign("aptDir.Available",TRUE,affylmGUIenvironment)
assign("aptDir", aptDir ,affylmGUIenvironment)
} else{
assign("aptDir.Available",FALSE,affylmGUIenvironment)
assign("aptDir", tt ,affylmGUIenvironment)
}
assign("cosie.Available", FALSE ,affylmGUIenvironment)
assign("EG2probeset.available", FALSE, affylmGUIenvironment)
assign("EG2probeset", tt, affylmGUIenvironment)
assign("exonAffyData.Available",FALSE,affylmGUIenvironment)
assign("exonAffyData", tt ,affylmGUIenvironment)
assign("dabg.Available" , FALSE, affylmGUIenvironment)
assign("dabg.p" , tt, affylmGUIenvironment)
assign("midas.p" , tt, affylmGUIenvironment)
assign("midas.p.Available" , FALSE, affylmGUIenvironment)
assign("spliceIndexData.Available",FALSE,affylmGUIenvironment)
assign("spliceIndexData", tt ,affylmGUIenvironment)
assign("AltSplRP.e.p" , tt, affylmGUIenvironment)
assign("AltSplRP.e.Available" , FALSE, affylmGUIenvironment)
assign("AltSplRP.g" , tt, affylmGUIenvironment)
assign("AltSplRP.g.Available" , FALSE, affylmGUIenvironment)
assign("mapping2ensembl" , tt, affylmGUIenvironment)
assign("mapping2ensembl.Available" , FALSE, affylmGUIenvironment)
assign("exonsSpecific2as" , tt, affylmGUIenvironment)
assign("exonsSpecific2as.Available" , FALSE, affylmGUIenvironment)
Try(assign("fitExon",tt,affylmGUIenvironment))
Try(assign("LinearModelFitExon.Available",FALSE,affylmGUIenvironment))
Try(assign("AltSplLimma" , tt, affylmGUIenvironment))
Try(assign("AltSplLimma.Available" , FALSE, affylmGUIenvironment))
Try(assign("intronicBg.available", TRUE,affylmGUIenvironment))
Try(assign("intronicBg", tt,affylmGUIenvironment))
assign("maSigProSigs.Available",FALSE,affylmGUIenvironment)
assign("Pset.Available",FALSE,affylmGUIenvironment)
assign("MLdesign.Available",FALSE,affylmGUIenvironment)
assign("MLdesign", tt ,affylmGUIenvironment)
assign("trainAffyData.available", FALSE, env=affylmGUIenvironment)
assign("testAffyData.available", FALSE, env=affylmGUIenvironment)
#NGS data
assign("NGS", tt ,affylmGUIenvironment)
assign("NGS.Available", FALSE, env=affylmGUIenvironment)
assign("NGSconversion.available", FALSE, env=affylmGUIenvironment)
assign("Genominator.Available", FALSE, env=affylmGUIenvironment)
assign("GenominatorDB",tt,affylmGUIenvironment)
assign("NGSscaling.Available", FALSE, env=affylmGUIenvironment)
assign("NGSprimaryMapping", tt ,affylmGUIenvironment) #used to know the type of data format to be loaded
assign("NGSprimaryMapping.Available", FALSE, env=affylmGUIenvironment)
#this should be updated also in the NewLimmafile because if a new project is loaded these variables
#are not initialized it would be better to make them in a function
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","maSIgProData" ,text="maSigPro results",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","maSIgProData","maSIgProData.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","PLM" ,text="PLM data",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","PLM","PLM.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","ExonArrays" ,text="Normalized Exon data from Expression Console",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","ExonArrays","ExonArrays.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AptDabg" ,text="APT DABG",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AptDabg","AptDabg.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AptMidas" ,text="APT MiDAS",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AptMidas","AptMidas.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","spliceIndex" ,text="Splice Index",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","spliceIndex","spliceIndex.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AltSplRP" ,text="Alternative Splicing by RP",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AltSplRP","AltSplRP.e.Status" ,text="Not Available at exon level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AltSplRP","AltSplRP.g.Status" ,text="Not Available at gene level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","metaData" ,text="Meta analysis",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","metaData","metaData.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","classification" ,text="Classification Params",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","classification","classification.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","LinearModelFitExon" ,text="Limma exon-level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","LinearModelFitExon","LinearModelFitExon.Status",text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","NGS" ,text="NGS data",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","NGS","NGS.Status",text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
#remember the previous part should be updated also down in the else in this function and
# in the NewLimmaFile and OpenLimmaFile function selection affy/exon/large/geo
assign("Pset" , tt, affylmGUIenvironment)
#Try(changes())
} else {
affylmGUI()
initialize.extAffylmGUI()
tt <- ""
assign("unfilteredData.location", tt, affylmGUIenvironment)
assign("whichArrayPlatform", tt,affylmGUIenvironment)#this will be set by the loaded platform 3'IVT, exons, illumina, AB1700
assign("geoPlatform", tt, env=affylmGUIenvironment)
assign("metaData.Available",FALSE,affylmGUIenvironment)
assign("metaData",tt,affylmGUIenvironment)
assign("exprConsoleLibs.Available",FALSE,affylmGUIenvironment)
assign("exprConsoleLibs", tt ,affylmGUIenvironment)#locate here the library files as a list of data.frames
#gathering affy libs and apt tools folders
Try(localdata <- paste(path.package("oneChannelGUI", quiet = FALSE), "/etc/localData.txt", sep=""))
Try(myinfo <- read.table(localdata, sep="\t", header=F, as.is=T))
Try(javaDir <- myinfo[which(myinfo[,1]=="javaDir"),2])
if(is.na(javaDir)){
Try(javaDir <- tt)
Try(assign("javaDir",javaDir,affylmGUIenvironment))
Try(assign("javaDir.Available",FALSE,affylmGUIenvironment))
} else if(javaDir == ""){
assign("javaDir", javaDir, affylmGUIenvironment)#directory where java is located
assign("javaDir.Available",FALSE,affylmGUIenvironment)
} else if(javaDir != ""){
assign("javaDir", javaDir, affylmGUIenvironment)#directory where java is located
assign("javaDir.Available",TRUE,affylmGUIenvironment)
}
Try(binDir <- myinfo[which(myinfo[,1]=="binDir"),2])
if(is.na(binDir)) {
Try(binDir <- tt)
Try(assign("binDir",binDir,affylmGUIenvironment))
Try(assign("binDir.Available",FALSE,affylmGUIenvironment))
} else if(binDir == ""){
assign("binDir", binDir, affylmGUIenvironment)#bin dir
assign("binDir.Available",FALSE,affylmGUIenvironment)
} else if(binDir != ""){
assign("binDir", binDir, affylmGUIenvironment)#bin dir
assign("binDir.Available",TRUE,affylmGUIenvironment)
}
Try(libDirLocation <- myinfo[which(myinfo[,1]=="libDirLocation"),2])
if(is.na(libDirLocation)) {
Try(libDirLocation <- tt)
Try(assign("libDirLocation",libDirLocation,affylmGUIenvironment))
Try(assign("libDir.Available",FALSE,affylmGUIenvironment))
}else if(libDirLocation == ""){
assign("libDirLocation", libDirLocation, affylmGUIenvironment)#directory where exon data are located
assign("libDirLocation.Available",FALSE,affylmGUIenvironment)
}else if(libDirLocation != ""){
assign("libDirLocation", libDirLocation, affylmGUIenvironment)#directory where exon data are located
assign("libDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(meVDirLocation <- myinfo[which(myinfo[,1]=="meVDirLocation"),2])
if(is.na(meVDirLocation)){
Try(meVDirLocation <- tt)
Try(assign("meVDirLocation",meVDirLocation,affylmGUIenvironment))
Try(assign("meVDirLocation.Available",FALSE,affylmGUIenvironment))
} else if(meVDirLocation == ""){
assign("meVDirLocation", meVDirLocation, affylmGUIenvironment)#directory where meV program is located
assign("meVDirLocation.Available",FALSE,affylmGUIenvironment)
} else if(meVDirLocation != ""){
assign("meVDirLocation", meVDirLocation, affylmGUIenvironment)#directory where meV program is located
assign("meVDirLocation.Available",TRUE,affylmGUIenvironment)
}
#needed for Affymetrix gene arrays
Try(assign("geneLibsInfo", tt ,affylmGUIenvironment))
#Try(perlDirLocation <- myinfo[which(myinfo[,1]=="perlDirLocation"),2]) #loacation of per ngs scripts
#Try(if(is.na(perlDirLocation)) perlDirLocation <- tt)
Try(perlDirLocation <- paste(path.package("oneChannelGUI", quiet = F),"/perl_scripts/", sep=""))
Try(assign("perlDirLocation",perlDirLocation,affylmGUIenvironment))
Try(assign("perlDirLocation.Available",TRUE,affylmGUIenvironment))
Try(pythonDirLocation <- paste(path.package("oneChannelGUI", quiet = F),"/inst/python_scripts/", sep=""))
Try(assign("pythonDirLocation",pythonDirLocation,affylmGUIenvironment))
Try(assign("pythonDirLocation.Available",TRUE,affylmGUIenvironment))
# if(perlDirLocation != ""){
# assign("perlDirLocation", perlDirLocation, affylmGUIenvironment)#directory where ngs perl scripts are located
# assign("perlDirLocation.Available",TRUE,affylmGUIenvironment)
# }
Try(tophatDirLocation <- myinfo[which(myinfo[,1]=="tophatDirLocation"),2]) #loacation of tophat
if(is.na(tophatDirLocation)) {
Try(tophatDirLocation <- tt)
Try(assign("tophatDirLocation",tophatDirLocation,affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(tophatDirLocation=="") {
Try(assign("tophatDirLocation",tt,affylmGUIenvironment))
Try(assign("tophatDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (tophatDirLocation != ""){
assign("tophatDirLocation", tophatDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("tophatDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(cuffDirLocation <- myinfo[which(myinfo[,1]=="cuffDirLocation"),2]) #loacation of cuff
if(is.na(cuffDirLocation)) {
Try(cuffDirLocation <- tt)
Try(assign("cuffDirLocation",cuffDirLocation,affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(cuffDirLocation=="") {
Try(assign("cuffDirLocation",tt,affylmGUIenvironment))
Try(assign("cuffDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (cuffDirLocation != ""){
assign("cuffDirLocation", cuffDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("cuffDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(samtoolsDirLocation <- myinfo[which(myinfo[,1]=="samtoolsDirLocation"),2]) #loacation of tophat
if(is.na(samtoolsDirLocation)) {
Try(samtoolsDirLocation <- tt)
Try(assign("samtoolsDirLocation",samtoolsDirLocation,affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(samtoolsDirLocation=="") {
Try(assign("samtoolsDirLocation",tt,affylmGUIenvironment))
Try(assign("samtoolsDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (samtoolsDirLocation != ""){
assign("samtoolsDirLocation", samtoolsDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("samtoolsDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(fastqcDirLocation <- myinfo[which(myinfo[,1]=="fastqcDirLocation"),2]) #loacation of tophat
if(is.na(fastqcDirLocation)) {
Try(fastqcDirLocation <- tt)
Try(assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment))
Try(assign("fastqcDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(fastqcDirLocation=="") {
Try(assign("fastqcDirLocation",tt,affylmGUIenvironment))
Try(assign("fastqcDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (fastqcDirLocation != ""){
assign("fastqcDirLocation", fastqcDirLocation, affylmGUIenvironment)#directory where tophat is located
assign("fastqcDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(bowtieDirLocation <- myinfo[which(myinfo[,1]=="bowtieDirLocation"),2]) #loacation of bowtie
if(is.na(bowtieDirLocation)) {
Try(bowtieDirLocation <- tt)
Try(assign("bowtieDirLocation",bowtieDirLocation,affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(bowtieDirLocation=="") {
Try(assign("bowtieDirLocation",tt,affylmGUIenvironment))
Try(assign("bowtieDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (bowtieDirLocation != ""){
assign("bowtieDirLocation", bowtieDirLocation, affylmGUIenvironment)#directory where bowtie is located
assign("bowtieDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(shrimpDirLocation <- myinfo[which(myinfo[,1]=="shrimpDirLocation"),2]) #loacation of shrimp
if(is.na(shrimpDirLocation)) {
Try(shrimpDirLocation <- tt)
Try(assign("shrimpDirLocation",shrimpDirLocation,affylmGUIenvironment))
Try(assign("shrimpDirLocation.Available",FALSE,affylmGUIenvironment))
}else if(shrimpDirLocation=="") {
Try(assign("shrimpDirLocation",tt,affylmGUIenvironment))
Try(assign("shrimpDirLocation.Available",FALSE,affylmGUIenvironment))
}else if (shrimpDirLocation != ""){
assign("shrimpDirLocation", shrimpDirLocation, affylmGUIenvironment)#directory where shrimp is located
assign("shrimpDirLocation.Available",TRUE,affylmGUIenvironment)
}
Try(bowtieRefs <- myinfo[which(myinfo[,1]=="bowtieRefs"),2])
Try(bowtieRefs <- as.vector(unlist(strsplit(bowtieRefs, ","))))
Try(names(bowtieRefs) <- c("hg19","mm9","rn4"))
Try(assign("bowtieRefs",bowtieRefs,affylmGUIenvironment))
assign("libDir", libDirLocation ,affylmGUIenvironment)#locate here the library files as a list of data.frames
assign("whichLib", tt ,affylmGUIenvironment)#remember the type of exon library loaded
assign("miRname", tt ,affylmGUIenvironment)
assign("miRname.available", FALSE,affylmGUIenvironment)
Try(aptDir <- myinfo[which(myinfo[,1]=="aptDir"),2])
Try(if(is.na(aptDir)) aptDir <- tt)
if(aptDir != ""){
assign("aptDir.Available",TRUE,affylmGUIenvironment)
assign("aptDir", aptDir ,affylmGUIenvironment)
} else{
assign("aptDir.Available",FALSE,affylmGUIenvironment)
assign("aptDir", tt ,affylmGUIenvironment)
}
assign("cosie.Available", FALSE ,affylmGUIenvironment)
assign("EG2probeset.available", FALSE, affylmGUIenvironment)
assign("EG2probeset", tt, affylmGUIenvironment)
assign("exonAffyData.Available",FALSE,affylmGUIenvironment)
assign("exonAffyData", tt ,affylmGUIenvironment)
assign("dabg.Available" , FALSE, affylmGUIenvironment)
assign("dabg.p" , tt, affylmGUIenvironment)
assign("midas.p" , tt, affylmGUIenvironment)
assign("midas.p.Available" , FALSE, affylmGUIenvironment)
assign("spliceIndexData.Available",FALSE,affylmGUIenvironment)
assign("spliceIndexData", tt ,affylmGUIenvironment)
assign("AltSplRP.e.p" , tt, affylmGUIenvironment)
assign("AltSplRP.e.Available" , FALSE, affylmGUIenvironment)
assign("AltSplRP.g" , tt, affylmGUIenvironment)
assign("AltSplRP.g.Available" , FALSE, affylmGUIenvironment)
assign("mapping2ensembl" , tt, affylmGUIenvironment)
assign("mapping2ensembl.Available" , FALSE, affylmGUIenvironment)
assign("exonsSpecific2as" , tt, affylmGUIenvironment)
assign("exonsSpecific2as.Available" , FALSE, affylmGUIenvironment)
Try(assign("fitExon",tt,affylmGUIenvironment))
Try(assign("LinearModelFitExon.Available",FALSE,affylmGUIenvironment))
Try(assign("AltSplLimma" , tt, affylmGUIenvironment))
Try(assign("AltSplLimma.Available" , FALSE, affylmGUIenvironment))
Try(assign("intronicBg.available", TRUE,affylmGUIenvironment))
Try(assign("intronicBg", tt,affylmGUIenvironment))
assign("maSigProSigs.Available",FALSE,affylmGUIenvironment)
assign("Pset.Available",FALSE,affylmGUIenvironment)
assign("MLdesign.Available",FALSE,affylmGUIenvironment)
assign("MLdesign", tt ,affylmGUIenvironment)
assign("trainAffyData.available", FALSE, env=affylmGUIenvironment)
assign("testAffyData.available", FALSE, env=affylmGUIenvironment)
#NGS data
assign("NGS", tt ,affylmGUIenvironment)
assign("NGS.Available", FALSE, env=affylmGUIenvironment)
assign("NGSconversion.available", FALSE, env=affylmGUIenvironment)
assign("Genominator.Available", FALSE, env=affylmGUIenvironment)
assign("GenominatorDB",tt,affylmGUIenvironment)
assign("NGSscaling.Available", FALSE, env=affylmGUIenvironment)
assign("NGSprimaryMapping", tt ,affylmGUIenvironment)
assign("NGSprimaryMapping.Available", FALSE, env=affylmGUIenvironment)
#this should be updated also in the NewLimmafile because if a new project is loaded these variables
#are not initialized it would be better to make them in a function
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","maSIgProData" ,text="maSigPro results",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","maSIgProData","maSIgProData.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","PLM" ,text="PLM data",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","PLM","PLM.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","ExonArrays" ,text="Normalized Exon data from Expression Console",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","ExonArrays","ExonArrays.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AptDabg" ,text="APT DABG",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AptDabg","AptDabg.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AptMidas" ,text="APT MiDAS",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AptMidas","AptMidas.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","spliceIndex" ,text="Splice Index",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","spliceIndex","spliceIndex.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","AltSplRP" ,text="Alternative Splicing by RP",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AltSplRP","AltSplRP.e.Status" ,text="Not Available at exon level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","AltSplRP","AltSplRP.g.Status" ,text="Not Available at gene level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","metaData" ,text="Meta analysis",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","metaData","metaData.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","classification" ,text="Classification Params",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","classification","classification.Status" ,text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","LinearModelFitExon" ,text="Limma exon-level",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","LinearModelFitExon","LinearModelFitExon.Status",text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
#NGS
Try(tkinsert(.affylmGUIglobals$mainTree,"end","root","NGS" ,text="NGS data",font=.affylmGUIglobals$affylmGUIfontTree))
Try(tkinsert(.affylmGUIglobals$mainTree,"end","NGS","NGS.Status",text="Not Available",font=.affylmGUIglobals$affylmGUIfontTree))
#remember the previous part should be updated also down in the else in this function and
# in the NewLimmaFile and OpenLimmaFile function selection affy/exon/large/geo
assign("Pset" , tt, affylmGUIenvironment)
#Try(changes())
})
}
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