readNarrowPeak: A function to read the Encode formatted narrowPeak file into...

Description Usage Arguments Value Examples

View source: R/readData.R

Description

A function to read the Encode formatted narrowPeak file into a GRanges object

Usage

1
readNarrowPeak(file, track.line=FALSE, zero.based=TRUE)

Arguments

file

an absolute or relative path to a bed file formatted by the Encode narrowPeak standard. The file can end in .gz, .bz2, .xz, or .zip and/or start with http:// or ftp://. If the file is not compressed it can also start with https:// or ftps://.

track.line

the number of track lines to skip, "auto" to detect them automatically or FALSE(default) if the bed file doesn't have track lines

zero.based

a boolean which tells whether the ranges in the bed file are 0 or 1 base encoded. (Default: TRUE)

Value

a GRanges object

Examples

1
2
3
4
narrow.peak.file = system.file('extdata',"ex.narrowPeak", package='genomation')
                 
narrow.peak = readBroadPeak(narrow.peak.file)
head(narrow.peak)

BIMSBbioinfo/genomation documentation built on Feb. 4, 2018, 12:11 p.m.