shiftGAlignmentsList: shift 5' ends

In jaime11/Transcription-Factor-Footprinting: ATAC-seq Quality Control

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")

jaime11/Transcription-Factor-Footprinting documentation built on May 31, 2019, 8:48 p.m.