readBroadPeak {genomation} | R Documentation

## A function to read the Encode formatted broad peak file into a GRanges object

### Description

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

### Usage

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

### Arguments

`file` | an absolute or relative path to a bed file formatted by the Encode broadPeak 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

    broad.peak.file = system.file('extdata',"ex.broadPeak", package='genomation')

    broad.peak = readBroadPeak(broad.peak.file)
    head(broad.peak)

[Package genomation version 1.24.0 Index]