GetCounts: GetCounts it estimate the gene counts wrapping the...

In elmerfer/ArribaR: gene Expression quantification, Gene Fusion detection and Immuno Content Deconvolution by STAR and ARRIBA softwares

GetCounts it estimate the gene counts wrapping the Rsubread::featureCounts function

Description

GetCounts it estimate the gene counts wrapping the Rsubread::featureCounts function

Usage

ft <- GetCounts("my.aligned_bam", feature = "exon")

Arguments

sbjBAM	the BAM file name
feature	string indicating if exons or genes are returned
annotSource	string possible values are "GENCODE19" or "inbuilt". If GENECODE19, it will use GENOCDE from Arriba software, if "inbuilt" it will use as in featureCounts
nthreads	integer, total of treads to use, default parallel::detectCores() -1

Value

an extended object as returned by featureCounts, the extension include in the targets slots the feature extracted (exon or gene)

Examples

## Not run: 
test.subject <- GetArribaRTest()
bam.subject <- RunSTAR(test.subject)
ft <- GetCounts(bam.subject)

## End(Not run)

elmerfer/ArribaR documentation built on Nov. 14, 2023, 1 p.m.