GetPSI_FromTranRef: GetPSI_FromTranRef

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

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

jpromeror/EventPointer documentation built on May 17, 2023, 10:29 p.m.