GetPSI_FromTranRef {EventPointer} | R Documentation |
Get the values of PSI.A filer expresion is applied if the user select the option of filter.
GetPSI_FromTranRef(PathsxTranscript, Samples, Filter = TRUE, Qn = 0.25)
PathsxTranscript |
the outpu of EventGTFfromTrancriptomeGTF |
Samples |
the samples (in the rowname of the samples must be written only the name of the transcript) |
Filter |
Boolean variable to indicate if an expression filter is applied. Defaul T |
Qn |
Quantile used to filter the events (Bounded between 0-1, Q1 would be 0.25). |
The output of the function is a list containing two elements: a matrix with the values of PSI and a list containing as many matrices as number of events. In each matrix is stored the expression of the different paths of an event along the samples.
data(EventXtrans) PathFiles <- system.file('extdata',package='EventPointer') filesnames <- dir(paste0(PathFiles,'/output')) PathFiles <- dir(paste0(PathFiles,'/output'),full.names = TRUE) dirtoload <- paste0(PathFiles,'/','abundance.tsv') RNASeq <- read.delim(dirtoload[1],sep = '\t', colClasses = c(NA,'NULL','NULL','NULL',NA)) for (n in 2:length(dirtoload)){ RNASeq[,n+1] <- read.delim(dirtoload[n],sep = '\t', colClasses = c('NULL','NULL','NULL','NULL',NA)) } rownames(RNASeq)<-RNASeq[,1] RNASeq<-RNASeq[,-1] colnames(RNASeq) <- filesnames rownames(RNASeq) <- sapply(strsplit(rownames(RNASeq),'\\|'),function(X) return(X[1])) RNASeq<-as.matrix(RNASeq) #must be a matrix variable #Obtain values of PSI PSIss <- GetPSI_FromTranRef(PathsxTranscript = EventXtrans,Samples = RNASeq,Filter = FALSE) PSI <- PSIss$PSI Expression <- PSIss$ExpEvs