PrepareBam_EP: Bam files preparation for EventPointer

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

Bam files preparation for EventPointer

Description

Prepares the information contained in .bam files to be analyzed by EventPointer

Usage

PrepareBam_EP(
  Samples,
  SamplePath,
  Ref_Transc = "Ensembl",
  fileTransc = NULL,
  cores = 1,
  Alpha = 2
)

Arguments

Samples	Name of the .bam files to be analyzed (Sample1.bam,Sample2.bam,...,etc).
SamplePath	Path where the bam files are stored.
Ref_Transc	Reference transcriptome used to name the genes found in bam files. Options are: Ensembl, UCSC or GTF.
fileTransc	Path to the GTF reference transcriptome ff Ref_Transc is GTF.
cores	Number of cores used for parallel processing.
Alpha	Internal SGSeq parameter to include or exclude regions

Value

SGFeaturesCounts object. It contains a GRanges object with the corresponding elements to build the different splicing graphs found and the counts related to each of the elements.

Examples

## Not run: 
 # Obtain the samples and directory for .bam files

   BamInfo<-si
   Samples<-BamInfo[,2]
   PathToSamples <- system.file('extdata/bams', package = 'SGSeq')
   PathToGTF<-paste(system.file('extdata',package='EventPointer'),'/FBXO31.gtf',sep='')

  # Run PrepareBam function
   SG_RNASeq<-PrepareBam_EP(Samples=Samples,
                            SamplePath=PathToSamples,
                            Ref_Transc='GTF',
                            fileTransc=PathToGTF,
                            cores=1)

## End(Not run)

jpromeror/EventPointer documentation built on March 5, 2025, 1:31 p.m.