[BioC] merging GRange objects

[Hervé Pagès]

Hi Murli,

On 06/24/2013 04:55 PM, Murli [guest] wrote:
>
> Hi,
>
> I would appreciate if you could tell me if the way I am merging the GappedAlignments object and GRanges objects is correct. mate1 and mate2 are GappedAlignment objects. I am merging them in order to associate my reads with the annotation.
>
> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
>
> mate.range= GRanges(seqnames(mate1[isSameCzome]),IRanges(start(mate1[isSameCzome])-offset,start(mate1[isSameCzome])+offset))
>
> codingRegions = refLocsToLocalLocs(mate.range, txdb)
>
> trans.info=select(txdb, key=values(codingRegions)$TXID, cols=c("GENEID","TXNAME"), keytype="TXID")
>
> trans.names=select(org.Hs.eg.db, trans.info$GENEID, c("GENENAME", "SYMBOL"))
>
> mrg.data1=merge(as.data.frame(trans.names), as.data.frame(trans.info), by.x="ENTREZID", by.y="GENEID")
>
> mrg.data2=merge(mrg.data1, as.data.frame(codingRegions), by.x="TXID", by.y="TXID")

It looks like you are merging data.frames, not GappedAlignments or
GRanges objects. Also you say that 'mate1' and 'mate2' are
GappedAlignments objects but I only see 'mate1' in the above code.

The exact meaning of "merging" depends on the objects involved.
Sometimes people use the term "merging" when they actually want
to combine or bind objects together with c(), rbind() or cbind().
Note that since GRanges and GappedAlignments objects are conceptually
vector-like objects of dimension 1, only c() works on them. That is,
rbind(), cbind(), and merge() (which are typically operating on 2-D
objects) are not supported on those objects.

Cheers,
H.

>
> Thanks ../Murli
>
>
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-redhat-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] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] biomaRt_2.16.0
>   [2] org.Hs.eg.db_2.9.0
>   [3] RSQLite_0.11.4
>   [4] DBI_0.2-7
>   [5] VariantAnnotation_1.6.6
>   [6] Rsamtools_1.12.3
>   [7] BSgenome.Hsapiens.UCSC.hg19_1.3.19
>   [8] BSgenome_1.28.0
>   [9] Biostrings_2.28.0
> [10] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2
> [11] GenomicFeatures_1.12.2
> [12] AnnotationDbi_1.22.6
> [13] Biobase_2.20.0
> [14] GenomicRanges_1.12.4
> [15] IRanges_1.18.1
> [16] BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-5       RCurl_1.95-4.1     rtracklayer_1.20.2 stats4_3.0.1
> [5] tcltk_3.0.1        tools_3.0.1        XML_3.98-1.1       zlibbioc_1.6.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> 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
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319