If you just need to merge the Val from obj2 as a column in obj1, i.e.,
there is no need to add ranges from obj2 to obj1, then it's simple using
match(). If you need the equivalent of merge(all=TRUE), then you need to
convert to data frames, use merge() and convert back. There is a
merge,VRanges method that does this. Nothing for GRanges yet though.


On Wed, Oct 16, 2013 at 7:15 AM, John linux-user <johnlinuxuser@yahoo.com>wrote:

> Hello everyone,
>
> I am wondering how to simply merge two GRanges objects by range field and
> add the value by additional vector. For example, I have two objects below
>
> obj1
>
> seqnames           ranges strand |       Val
>             <Rle>        <IRanges>  <Rle> | <integer>
>   [1] chr1_random [272531, 272571]      + |        88
>   [2] chr1_random [272871, 272911]      + |        45
>
> obj2
>  seqnames           ranges strand |       Val
>             <Rle>        <IRanges>  <Rle> | <integer>
>   [1] chr1_random [272531, 272581]      + |        800
>   [2] chr1_random [272850, 272911]      + |        450
>
> after merged, it should be an object as the following mergedObject and it
> would concern the differences in IRANGE data (e.g. 581 and 850 in obj2
> above were different from those of obj1, which were 571 and 871
> respectively)
>
> mergedObject
>
>  seqnames           ranges strand                 |         object2Val
> object1Val
>             <Rle>        <IRanges>  <Rle>         |         <integer>
> <integer>
>   [1] chr1_random [272531, 272581]      + |        800               88
>   [2] chr1_random [272850, 272911]      + |        450               45
>
>
>
>
> On Tuesday, October 15, 2013 12:36 PM, 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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>         [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

