gff {mixer}R Documentation

write out peaks in gff format

Description

write the output of function mergeWindows into a gff file, which can be displayed by NimbleGen software SignalMap

Usage

gff(mpks, file, source="ChIP", feature=".", strand="+", frame=".", 
 separate.att=FALSE)

Arguments

mpks peaks, from funcion merge.window
file output file name
source value for source column in gff file
feature value for feature column in gff file
strand value for strand column in gff file
frame value for frame column in gff file
separate.att By default, separate.att=FALSE, then the number of probes and the correponding lfdr are combined as one attribute. If separate.att=TRUE, the number of probes and the correponding lfdr are two separate columns in the output file. This format is eaiser to use for following analysis, but cannot be displayed by SignalMap since it has an extra column.

Author(s)

Wei Sun

See Also

mergeWindow


[Package mixer version 1.03 Index]