GetPSI_FromTranRef {EventPointer}R Documentation

GetPSI_FromTranRef

Description

Get the values of PSI.A filer expresion is applied if the user select the option of filter.

Usage

GetPSI_FromTranRef(PathsxTranscript, Samples, Filter = TRUE, Qn = 0.25)

Arguments

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).

Value

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.

Examples

   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


[Package EventPointer version 2.8.0 Index]