PrepareBam_EP {EventPointer} | R Documentation

## 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)

[Package EventPointer version 3.2.0 Index]