readBroadPeak {genomation} | R Documentation |
A function to read the Encode formatted broad peak file into a GRanges object
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 |
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)