Hi Lichun, On Mon, Aug 23, 2010 at 4:14 PM, Jiang, Lichun (NIH/NIDDK) [F] <[email protected]> wrote: > Hi Dear all, > I am a newbie using GRanges and related packages. Try to figure out how > can I add an column of values to the GenomicRanges. > > For example I get a object named as TF_peaks: > > GRanges with 2000 ranges and 3 elementMetadata values > seqnames ranges strand | elementMetadata.polIIsignal > elementMetadata.inputSignal elementMetadata.enrichment > <Rle> <IRanges> <Rle> | <integer> > <integer> <numeric> > [1] chr1 [205566106, 205576720] * | 1504 > 4 382.2567 > [2] chr1 [ 11890546, 11892791] * | 1140 > 4 347.6909 > .... > > I tried to add another value to describe whether this features are > overlapping with promoters(I already has this value as inpromoteres for > example ). > But I can't add this value to the TF_peaks object by standard function for > dataframe manipulation. I guess I am not fully understand the S4 methods. > Anyone can help me out?
How did you try to do it? You have to "get" the DataFrame associated with your GRanges object using the `values` or `elementMetadata` function, which you could then manipulate as you (probably) are expecting to. So, you simply have to: R> values(TF_peas)$overlaps <- inpromoteres or variation above, given the column name you want to store this under, and the variable name you have your 'overlapping' info in. Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
