[BioC] Using Precede in GenomicRanges
Martin Morgan
mtmorgan at fhcrc.org
Fri Apr 19 19:19:31 CEST 2013
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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