Hi Steve,
Thanks, it works!
Lichun
________________________________________
From: Steve Lianoglou [[email protected]]
Sent: Monday, August 23, 2010 5:00 PM
To: Jiang, Lichun (NIH/NIDDK) [F]
Cc: [email protected]
Subject: Re: [Bioc-sig-seq] adding columns to values of GenomicRange objects
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
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