Thanks Peter,

elementMetadata(gr)[["toAdd"]] = 1:10    worked for me.

Cheers!!!
Fahim


On Tue, Nov 15, 2011 at 8:46 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 11/15/2011 05:31 PM, Martin Morgan wrote:
>
>> On 11/15/2011 03:50 PM, Fahim Mohammad wrote:
>>
>>> Hi
>>> Is there a function to augment metadata into an already built GRanges
>>> object?
>>>
>>> For example (ex from vignette)
>>>
>>>
>>>  gr<- GRanges(seqnames = Rle(c("chr1", "chr2", "chr1",+ "chr3"), c(1,
>>>> 3, 2, 4)), ranges = IRanges(1:10, end = 7:16,+ names = head(letters,
>>>> 10)), strand = Rle(strand(c("-",+ "+", "*", "+", "-")), c(1, 2, 2, 3,
>>>> 2)), score = 1:10,+ GC = seq(1, 0, length = 10))
>>>>
>>>
>>  grGRanges with 10 ranges and 2 elementMetadata values:
>>> seqnames ranges strand | score GC
>>> <Rle> <IRanges> <Rle> |<integer> <numeric>
>>> a chr1 [ 1, 7] - | 1 1
>>> b chr2 [ 2, 8] + | 2 0.888888888888889
>>> c chr2 [ 3, 9] + | 3 0.777777777777778
>>> d chr2 [ 4, 10] * | 4 0.666666666666667
>>> e chr1 [ 5, 11] * | 5 0.555555555555556
>>> f chr1 [ 6, 12] + | 6 0.444444444444444
>>> g chr3 [ 7, 13] + | 7 0.333333333333333
>>> h chr3 [ 8, 14] + | 8 0.222222222222222
>>> i chr3 [ 9, 15] - | 9 0.111111111111111
>>> j chr3 [10, 16] - | 10 0
>>> ---
>>> seqlengths:
>>> chr1 chr2 chr3
>>> NA NA NA
>>>
>>
>
>  toAdd = c(1:10)
>>
>
>
>  toAdd [1] 1 2 3 4 5
>>
>>> 6 7 8 9 10
>>>
>>
>
> oops, your email came through poorly formatted, I think you want
>
>  values(gr)[["toAdd"]] = 1:10
>
> or
>
>  values(gr)[,"toAdd"] = 1:10
>
> (equivalently, elementMetadata(gr)[["toAdd"]] = 1:10). values(gr) is
> returning a DataFrame, which can be manipulated like a standard R
> data.frame.
>
> Sorry about that, and hope I've got it right this time. Martin
>
>
>
>>> I want to append this ('toAdd') metadata to already built GRanges object
>>> ('gr').
>>> Is there any function to do that?
>>>
>>
>> Hi Fahim -- Along the lines of
>>
>>  > metadata(gr) = list("some thing")
>>  > metadata(gr) = c(metadata(gr), list("some other thing"))
>>  > metadata(gr)
>> [[1]]
>> [1] "some thing"
>>
>> [[2]]
>> [1] "some other thing"
>>
>> see ?"metadata<-".
>>
>> Martin
>>
>>  Thanks
>>>
>>> Thanks
>>> Fahim
>>> Bioinformatics Lab
>>> University of Louisville
>>> Louisville, KY USA
>>>
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>>>
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>>>
>>
>>
>>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
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