readBroadPeak: A function to read the Encode formatted broad peak file into...
In BIMSBbioinfo/genomation: Summary, annotation and visualization of genomic data

Description Usage Arguments Value Examples

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

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

`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)

a GRanges object

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