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]