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 >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: >>> http://news.gmane.org/gmane.**science.biology.informatics.**conduc tor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>> >> >> >> > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]]