Guitar (version 1.10.0)

narrowPeaktoGRanges: narrowPeaktoGRanges

Description

read the narrowpeak format from MACS software into GRangesList object.

NAME_peaks.narrowPeak is BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. You can load it to UCSC genome browser. Definition of some specific columns are: 5th: integer score for display 7th: fold-change 8th: -log10pvalue 9th: -log10qvalue 10th: relative summit position to peak start.

Usage

narrowPeaktoGRanges(file)

Arguments

file

a string specifies where the narrow peak file is located.

Value

A GRanges object will be returned.

References

MACS2 software: https://github.com/taoliu/MACS/tree/master/MACS2

Examples

narrowPeak=system.file("extdata", "m6A_hg19_1000peaks_macs2.narrowPeak", package="Guitar")
m6A_Bcell <- narrowPeaktoGRanges(narrowPeak) # bam imported as GAlignments
m6A_Bcell