1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
|
getWithinGeneExpression <- function(sampleFile, outFile=NULL, trInfo=NULL, trInfoFile=NULL, pretend=FALSE, keepOrder=FALSE){
if(!is.null(trInfo)){
if(!tri.hasGeneNames(trInfo))stop("The trInfo object does not contain necessary information.");
trInfoFile <- tempfile("data",fileext=c(".tr"));
if(!pretend){
tri.save(trInfo,trInfoFile);
} else{
message(paste(c("# Save trInfo object as ",trInfoFile," file.")));
}
}else {
if(is.null(trInfoFile)){
trInfoFile<-.changeExt(sampleFile);
}
}
if(!file.exists(trInfoFile)){
stop("Please provide valid transcript information either through trInfo object or trInfoFile file.");
}
if(!(pretend || tri.file.hasGeneNames(trInfoFile)))stop(paste(c("File ",trInfoFile," does not contain necessary information.")));
if(is.null(outFile)){
fName <- tail(unlist(strsplit(tail( unlist(strsplit(sampleFile,"/")),1),"\\\\")),1)
if(fName != ""){
outFile <- tempfile(paste(fName,"-",sep=""),fileext =".WGE");
}else{
outFile <- tempfile("dataBS-E-",fileext=".WGE");
}
}
args <- c('getWithinGeneExpression', sampleFile, '--outFile', outFile, '--trInfoFile', trInfoFile);
if(!keepOrder){
args <- c(args, '--groupByGene')
}
if(pretend){
writeLines(.specialPaste(args))
}else{
argc <- length(args);
result <- .C("_getWithinGeneExpression", as.integer(argc), as.character(args));
}
return(outFile);
}
|
