GetPSI_FromTranRef {EventPointer} | R Documentation |
Get the values of PSI. A filer expression is applied if the user select the option of filter.
GetPSI_FromTranRef( Samples, PathsxTranscript, Bootstrap = FALSE, Filter = TRUE, Qn = 0.25 )
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). |
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.
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