[BioC] Augmenting metadata values in GRanges object

[Martin Morgan]

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
>>
>> [[alternative HTML version deleted]]
>>
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>
>


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