shiftGAlignments {ATACseqQC} | R Documentation

## shift 5' ends for single end reads

### 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

    shiftGAlignments(gal, positive = 4L, negative = 5L, outbam)

### Arguments

`gal` | An object of GAlignments.
`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.

### 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,
                       what=c("qname", "flag", "mapq", "seq", "qual"),
                       which=which, asMates=FALSE, bigFile=TRUE)
    objs <- shiftGAlignments(gal)
    export(objs, "shift.bam")

[Package ATACseqQC version 1.12.5 Index]