[BioC] Using Precede in GenomicRanges

[Martin Morgan]

On 04/19/2013 08:45 AM, Valerie Obenchain wrote:
> 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]))

or just

    query$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]]
>>
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>>
>
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