PrepareBam_EP {EventPointer} | R Documentation |
Prepares the information contained in .bam files to be analyzed by EventPointer
PrepareBam_EP(Samples, SamplePath, Ref_Transc = "Ensembl", fileTransc = NULL, cores = 1, Alpha = 2)
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 |
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.
## 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)