On Wed, Oct 16, 2013 at 1:38 AM, Lukasz Kielpinski <cosiarz@gmail.com>wrote:

> It worked, the 'map' function was very helpful!
>
> In the end I implemented as you said with modifications:
> a) reassigned "chrM" is_circular to FALSE for mapping to work (I still use
> R 2.15)
>
> my_exons@unlistData@seqinfo@is_circular <- rep(FALSE, 35)
>
>
Please refrain from direct slot access. Something like
isCircular(seqinfo(my_exons)) <- FALSE



> b) reassigned start positions of motifsTX to 1 is below 1:
>
> start(motifsTX)[start(motifsTX)<=1] <- 1
>
>
or: restrict(motifsTX, 1)


> c) extracted sequences without ordering by mapping (motifsTX was already
> ordered) and using subseq function (" '[' subsetting by Ranges is defunct ")
>
> motifSeqs <- subseq(tx[subjectHits(mapping)], start=start(motifsTX),
> end=end(motifsTX))
>
>

Yea, the Ranges support for [ was re-incarnated last devel cycle. You
really should update.


Thanks a lot for the valuable hint!
>
> Lukasz
>
>
>
>
>
> On 15 October 2013 19:00, Michael Lawrence <lawrence.michael@gene.com>wrote:
>
>> Use map(gr, exonsByResult) to map your GRanges to transcript coordinates.
>> Then, do any range transformations like flank(). Use
>> GenomicFeatures::extractTranscriptsFromGenome to get the transcript
>> sequences. To extract those ranges from each sequence, use [, with some
>> repping. Should only be about 4 lines of code. Something like this:
>>
>> mapping <- map(motifsGR, exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene))
>> motifsTX <- flank(ranges(mapping), n)
>> tx <- extractTranscriptsFromGenome(Hsapiens,
>> TxDb.Hsapiens.UCSC.hg19.knownGene)
>> motifSeqs <- tx[subjectHits(mapping)][motifsTX[queryHits(mapping)]]
>>
>> Untested...
>>
>> Good luck,
>> Michael
>>
>>
>> On Tue, Oct 15, 2013 at 9:36 AM, Lukasz [guest] <guest@bioconductor.org>wrote:
>>
>>>
>>> Hi!
>>>
>>> Problem summary: How to retrieve part of the sequence of mRNA around
>>> given location.
>>>
>>> I have the locations of the binding to mRNA events as GRanges (GRevents)
>>> and need to retrieve sequence for motif finding. The problem is that if I
>>> use getSeq(flank(GRevents, width=n)) then I get the genomic sequence not
>>> transcript sequence, i.e. not accounting for introns or mRNA border. I have
>>> tried solving it with exonsBy("transcriptDb object", "tx") function but
>>> without success.
>>>
>>> Question: Is there a bioconductor-supported way of getting resolving the
>>> problem? With CLIPseq being more and more popular this will be very
>>> demanded function.
>>>
>>> Thanks,
>>> Lukasz
>>>
>>>  -- output of sessionInfo():
>>>
>>> > sessionInfo()
>>> R version 2.15.0 (2012-03-30)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>  [7] LC_PAPER=C                 LC_NAME=C
>>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>>  [1] rtracklayer_1.16.0                 GenomicFeatures_1.8.1
>>>  [3] AnnotationDbi_1.18.4               Biobase_2.16.0
>>>  [5] BSgenome.Mmusculus.UCSC.mm9_1.3.17 BSgenome_1.24.0
>>>  [7] Biostrings_2.24.1                  GenomicRanges_1.8.3
>>>  [9] IRanges_1.14.2                     BiocGenerics_0.2.0
>>>
>>> loaded via a namespace (and not attached):
>>>  [1] biomaRt_2.12.0  bitops_1.0-4.1  DBI_0.2-5       RCurl_1.91-1
>>>  [5] Rsamtools_1.8.0 RSQLite_0.11.1  stats4_2.15.0   tools_2.15.0
>>>  [9] XML_3.9-4       zlibbioc_1.2.0
>>>
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
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>>>
>>
>>
>

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