shiftGAlignmentsList: shift 5' ends

In jianhong/ATACseqQC: ATAC-seq Quality Control

shift 5' ends

Description

shift the GAlignmentsLists by 5' ends. All reads aligning to the positive strand will be offset by +4bp, and all reads aligning to the negative strand will be offset -5bp by default.

Usage

shiftGAlignmentsList(
  gal,
  positive = 4L,
  negative = 5L,
  outbam,
  BPPARAM = NULL,
  slidingWindowSize = 5e+07
)

Arguments

gal	An object of GAlignmentsList.
positive	integer(1). the size to be shift for positive strand
negative	integer(1). the size to be shift for negative strand
outbam	file path to save shift reads. If missing, no file will be write.
BPPARAM	The parallel parameters used by BiocParrallel.
slidingWindowSize	The width of each tile when the input is big file. By default 50e6, the memory cost will be about 6GB for each thread for a 5GB bam file. Increase the value will increase the memory cost but may speed up the process.

Value

An object of GAlignments with 5' end shifted reads. The PCR duplicated will be removed unless there is metadata keepDuplicates set to TRUE.

Author(s)

Jianhong Ou

Examples

bamfile <- system.file("extdata", "GL1.bam", package="ATACseqQC")
tags <- c("AS", "XN", "XM", "XO", "XG", "NM", "MD", "YS", "YT")
library(BSgenome.Hsapiens.UCSC.hg19)
which <- as(seqinfo(Hsapiens)["chr1"], "GRanges")
gal <- readBamFile(bamfile, tag=tags, which=which, asMates=TRUE)
objs <- shiftGAlignmentsList(gal)
export(objs, "shift.bam")
## Not run: 
  bamfile <- 'a.big.file.bam'
  tags <- c("NM", "MD")
  which <- GRanges(c('chr1:1-249250621:*', 'chr2:1-243199373:*'))
  gal <- readBamFile(bamfile, tag=tags, which=which, 
  asMates=TRUE, bigFile=TRUE)
  library(BiocParallel)
  BPPARAM <- MulticoreParam(workers = 2, progress=TRUE)
  objs <- shiftGAlignmentsList(gal, BPPARAM = BPPARAM,
   outbam="shift.bam")

## End(Not run)

jianhong/ATACseqQC documentation built on May 9, 2024, 2:21 p.m.