PrepareBam_EP: Bam files preparation for EventPointer

Description Usage Arguments Value Examples

View source: R/PrepareBam_EP.R

Description

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

Usage

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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

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## 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)

EventPointer documentation built on Nov. 8, 2020, 7:12 p.m.