GetPSI_FromTranRef {EventPointer} | R Documentation

## GetPSI_FromTranRef

### Description

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

### Usage

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

### Arguments

`Samples` | matrix or list containing the expression of the samples.
`PathsxTranscript` | the output of EventDetection_transcriptome.
`Bootstrap` | Boolean variable to indicate if bootstrap data from pseudo-alignment is used.
`Filter` | Boolean variable to indicate if an expression filter is applied. Default TRUE.
`Qn` | Quartile used to filter the events (Bounded between 0-1, Qn would be 0.25 by default).

### Value

The output 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)

         PathSamples <- system.file("extdata",package="EventPointer")
         PathSamples <- paste0(PathSamples,"/output")
         PathSamples <- dir(PathSamples,full.names = TRUE)

         data_exp <- getbootstrapdata(PathSamples = PathSamples,type = "kallisto")

         #same annotation
         rownames(data_exp[[1]]) <- gsub("\\|.*","",rownames(data_exp[[1]]))

         #Obtain values of PSI
         PSI_List <- GetPSI_FromTranRef(PathsxTranscript = EventXtrans,Samples = data_exp,Bootstrap = TRUE, Filter = FALSE)
         PSI <- PSI_List$PSI
         Expression_List <- PSI_List$ExpEvs

[Package EventPointer version 3.0.0 Index]