Nothing
## compute PPLR for two or more conditions
getDE <- function( conditions, outPrefix=NULL, samples=FALSE, trInfoFile=NULL, norm=NULL, seed=NULL, pretend=FALSE ){
## pretend needs prefix
if(pretend && is.null(outPrefix)){
message("In case of no outPrefix provided this function uses R temporary directories which are only valid during the current session.")
stop("Please provide outPrefix when using the pretend option.")
}
## check file extensions
ext <- .getExt(conditions[[1]][1]);
for(it in unlist(conditions)){
if(!file.exists(it))stop(paste("File",it,"does not exist"));
if(ext!=.getExt(it))stop(paste("File",it,"has different extension from first file."));
}
if(is.null(outPrefix)){
outPrefix <- tempfile("dataBS-DE-");
}
if(is.null(trInfoFile)){
trInfoFile=.changeExt(conditions[[1]][1]);
if(file.exists(trInfoFile)){
message(paste("## No trInfoFile provided, will try using",trInfoFile,"for result's row names."));
}else{
trInfoFile=NULL;
}
}
meanFile <- paste(outPrefix, "Lmean", sep=".");
parFile <- paste(outPrefix, "par", sep=".");
message("Computing overall mean.");
getMeanVariance(conditions,meanFile,log=TRUE,norm=norm,pretend=pretend);
message("Estimating hyperparameters.");
estimateHyperPar(parFile,conditions,meanFile=meanFile,norm=norm,seed=seed,pretend=pretend);
message("Estimating condition mean expression and PPLR.");
estimateDE(conditions,outPrefix,parFile,samples=samples,norm=norm,seed=seed,pretend=pretend);
if(samples){
samplesFiles = c();
for(i in 1:length(conditions)){
samplesFiles = c(samplesFiles, paste(outPrefix,"-C",(i-1),".est",sep=""));
}
}else{
samplesFiles = NULL;
}
pplrFN <- paste(outPrefix, "pplr", sep=".");
if(pretend){
data <- NULL
}else{
data <- loadSamples( pplrFN, trInfoFile);
condN <- length(conditions);
pplrList <- c();
fcList <- c();
meanList <- c();
for(i in 1:condN){
meanList <- c(meanList, paste("mean",i,sep=" "));
if(i == condN) break;
for(j in (i+1):condN){
pplrList <- c(pplrList, paste("pplr ",i,"~",j,sep=""));
fcList <- c(fcList, paste("log2FC ",i,"~",j,sep=""), "ciLow", "ciHigh");
}
}
colnames(data)<-c(pplrList, fcList, meanList);
}
return(list(pplr=data,fn=list(pplr=pplrFN,samplesFiles=samplesFiles)));
}
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