narrowPeaktoGRanges {Guitar} | R Documentation

## 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

[Package Guitar version 1.18.0 Index]