shiftGAlignmentsList {ATACseqQC}R Documentation

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)

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

Value

An object of GAlignments with 5' end shifted reads.

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")

[Package ATACseqQC version 1.6.4 Index]