gff {mixer} | R Documentation |
write the output of function mergeWindows into a gff file, which can be displayed by NimbleGen software SignalMap
gff(mpks, file, source="ChIP", feature=".", strand="+", frame=".", separate.att=FALSE)
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. |
Wei Sun