R/Run_get_results_from_JunctionSeq.R

In SCCC-BBC/GOSJ:

#Use JunctionSeq to get analysis results
GetResultsFromJunctionSeq<-function(dir.name,file.sample,file.count,file.gff){
#Get sample file
path.file.sample<-paste0(dir.name,file.sample)
decoder.bySample<-read.table(path.file.sample,header=T,stringsAsFactors = F)

#Get count file
path.file.count<-paste0(dir.name,decoder.bySample$sample.ID,file.count)
countFiles<-paste0(path.file.count)

#Get annotation file
path.file.gff<-file.gff

#Analysis
jscs.2<-runJunctionSeqAnalyses(sample.files= countFiles,sample.names= decoder.bySample$sample.ID,condition= decoder.bySample$group.ID,
                             flat.gff.file=path.file.gff,nCores=1,verbose=TRUE,debug.mode=TRUE,use.multigene.aggregates = TRUE)

return(jscs.2)
}