[BioC] Using Precede in GenomicRanges

[Valerie Obenchain]

Hello,

query <- GRanges("chr1", IRanges(c(5, 20), width=1))
subject <- GRanges("chr1", IRanges(c(30, 10, 1), width=1,
                                    names=c("gene1", "gene2")))
out <- precede(query, subject)
 > out
[1] 3 1

You can add metdata columns to a GRanges with 'mcols<-'. This assignment 
will replace any existing metadata columns with 'subjectNames'.
mcols(query) <- DataFrame(subjectNames=names(subject)[out])

If you want to keep the existing metadata columns, use append() on the 
right side:
mcols(query) <- append(mcols(query),
                        DataFrame(subjectNames=names(subject)[out]))



Valerie


On 04/19/2013 07:27 AM, Tom Oates wrote:
> Dear All
> I have GRanges objects of transcript information (subject) & for regions of
> interest (query).
> Top lines of (subject):
>       seqnames                 ranges strand   |     tx_id            tx_name
>               <Rle>              <IRanges>  <Rle>   | <integer>
> <character>
>        [1]        1          [5473, 16844]      +   |         1
> ENSRNOT00000044270
>        [2]        1          [5526, 16968]      +   |         2
> ENSRNOT00000049921
>        [3]        1          [5526, 16968]      +   |         3
> ENSRNOT00000051735
>        [4]        1          [5598, 13520]      +   |         4
> ENSRNOT00000034630
>        [5]        1          [8268, 16850]      +   |         5
> ENSRNOT00000044505
>        [6]        1          [8316, 17577]      +   |         6
> ENSRNOT00000042693
>        [7]        1          [8884, 16850]      +   |         7
> ENSRNOT00000044187
>        [8]        1          [8956,  9955]      +   |         8
> ENSRNOT00000041082
>        [9]        1          [9055, 17351]      +   |         9
> ENSRNOT00000050254
>
> Top lines of (query):
>          seqnames                 ranges strand
>              <Rle>              <IRanges>  <Rle>
>       [1]       10 [ 37958164,  37958165]      +   |
>       [2]        7 [ 46598224,  46598225]      -   |
>       [3]        1 [  9627018,   9627019]      -   |
>       [4]        9 [ 10158183,  10158184]      +   |
>       [5]        2 [185436985, 185436986]      +   |
>       [6]        8 [ 93638247,  93638248]      -   |
>       [7]        7 [ 68559015,  68559016]      -   |
>       [8]       12 [ 10978744,  10978745]      +   |
>       [9]       17 [ 33460790,  33460791]      -   |
>
> and am using the precede command to find the preceeding transcripts to my
> regions of interest
>
> output<-precede(query, subject, ignore.strand=FALSE)
>
> I am aware that the object called "output" is of class integer with the row
> names of "subject" which represent the preceding hits for "query", but I
> have so far been unable to use these row names to end up with a granges
> object with the name of the preceding transcripts as metadata in a granges
> object containing the ranges from "query" i.e something that would look
> like:
> [1]       10 [ 37958164,  37958165]      +   |ENSRNOT00000044270
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>