read_BAM: Read BAM files into R

In hyochoi/SCISSOR: Shape changes in selecting sample outliers in RNA-seq

Read BAM files into R

Description

Get coverage pileup from BAM files for the provided regions.

Usage

read_BAM(
  BAMfiles,
  caseIDs = NULL,
  gaf = NULL,
  symbol = NULL,
  regions = NULL,
  outputType = "part_intron",
  strand.specific = FALSE,
  ...
)

Arguments

BAMfiles	a list of BAM file names
caseIDs	a list of case IDs in order of BAMfiles
symbol	a gene symbol (gene name)
regions	genomic regions to read formatted as "chr1:1-100,200-300:+". See also build_gaf.
outputType	type of intronic region that will be included in output, with choices "whole_intron", "part_intron", or "only_exon"; the second is the default.
strand.specific	indicator to get only "+" strand pileup

Examples

regions="chr1:1-100,200-300:+"
start_time = Sys.time()
countPileup = read_BAM(BAMfiles=BAMfiles,caseIDs=caseIDs,regions=regions)
end_time = Sys.time()
end_time - start_time

hyochoi/SCISSOR documentation built on July 6, 2022, 6:59 a.m.