runFC: Run featureCounts on a set of bam files

Description Usage Arguments

View source: R/runFC.R

Description

Run featureCounts on a set of bam files

Usage

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runFC(projName, bamDir, fileList, outFile, ncores = 16,
  subreadMod = "apps/subread/1.5.0-p3/gcc-4.4.7",
  refDir = "/scratch/pschofield/ref/star/GRCh37_pa",
  annoFile = file.path(refDir, "Homo_sapiens.GRCh37.85.gtf"),
  genomeFile = file.path(refDir,
  "Homo_sapiens.GRCh37.dna_sm.primary_assembly.fa"),
  switches = " -M -O -C -P -p -t exon -g transcript_id -f -d 50")

Arguments

projName

project name

bamDir

location of bamfiles (actually directory where counting takes place)

fileList

list of files if not full paths will have to be in bamDir but can be fully qualified paths

outFile

name of output file

ncores

number of cores to use

annoFile

the gtf annotation file to count against must of course match the alignment reference

switches

extra switches for featureCounts for example paired end or exon counting


PietaSchofield/plibb documentation built on Nov. 11, 2018, 5:15 a.m.