GetPSI_FromTranRef: GetPSI_FromTranRef

In EventPointer: An effective identification of alternative splicing events using junction arrays and RNA-Seq data

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

EventPointer documentation built on Nov. 8, 2020, 7:12 p.m.