[BioC] TXNAME mapping

Sat Jun 22 17:09:19 CEST 2013

Hi Marc/James,

Many thanks for your prompt reply. My apologies for not posting the code.  Here is code. I guess, I messed up when I tried to merge it.  What I want to achieve is to determine what the reads corresponds to, i.e. whether it is in the coding region, promoter region, UTR as well as determine if there are any transcription factors that bind to the reads. 

bf.data= readGappedAlignments(bam_file, param=ScanBamParam(what=scanBamWhat()))

mate.pairs=table(mcols(bf.data)$qname)

onlyPairs=names(mate.pairs)[mate.pairs==2]

mappedPairs=bf.data[mcols(bf.data)$qname %in% onlyPairs]

mate1=mappedPairs[c(T,F)]

mate2=mappedPairs[c(F,T)]

isSameCzome= (seqnames(mate1)==seqnames(mate2))

offset=150

txdb = TxDb.Hsapiens.UCSC.hg19.knownGene

mate.range= GRanges(seqnames(mate1[isSameCzome])[1:1000],IRanges(start(mate1[isSameCzome])[1:1000]-offset,start(mate1[isSameCzome])[1:1000]+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"))

mate.range.df=as.data.frame(mate.range)

trans.info.df=as.data.frame(trans.info.df)

trans.names.df=as.data.frame(trans.names)

mrg.data=merge(trans.info.df,mate.range.df)

mrg.data=merge(mrg.data, trans.names.df)

Thanks for your help.

Cheers../murli

-----Original Message-----
From: Marc Carlson [mailto:mcarlson at fhcrc.org] 
Sent: Saturday, June 22, 2013 12:07 AM
To: Murli [guest]
Cc: bioconductor at r-project.org; Nair, Murlidharan T
Subject: Re: TXNAME mapping

Hi Murli,

I have no idea what you did since you didn't give me an example. In the future, you might find it helpful to look at the posting guide which you can find on our web site here:

http://www.bioconductor.org/help/mailing-list/posting-guide/

But from what you did tell me, my guess is that you just wanted to extract the information you listed.  Here is how I would do something like this:

library(Homo.sapiens)
select(Homo.sapiens,
            keys=c(63934,7038),
cols=c("TXID","GENEID","TXNAME","TXSTART","TXEND","TXCHROM","TXSTRAND"),
            keytype="ENTREZID")

Hope that this helps you,

   Marc

On 06/21/2013 07:16 PM, Murli [guest] wrote:
> Hi,
>
> I am annotating my reads using TxDb.Hsapiens.UCSC.hg19.knownGene and org.Hs.eg.db. I am able to get everything work and also merge the data, but when I reviewd the output I see that the same TXNAME is mapped to different locations. See part of the output below. TXNAME uc003ytw.3 is associated with chr8  13515402  13515702   301 and  chr12  71612488  71612788   301.  I thought it should be unique, I would appreciate if you could correct me if I am missing something in understanding TXNAME.
>
> Thanks ../Murli
>
>
>
>   
>> mrg.data[1000:1100,]
>        TXID GENEID     TXNAME seqnames     start       end width strand
> 1000 32071   7038 uc003ytw.3     chr8  13515402  13515702   301      *
> 1001 68728  63934 uc002qnd.3     chr8  14339379  14339679   301      *
> 1002 68729  63934 uc002qne.3     chr8  14339379  14339679   301      *
> 1003 68730  63934 uc010etm.3     chr8  14339379  14339679   301      *
> 1004 32071   7038 uc003ytw.3     chr8  14339379  14339679   301      *
> 1005 68728  63934 uc002qnd.3    chr12  71612488  71612788   301      *
> 1006 68729  63934 uc002qne.3    chr12  71612488  71612788   301      *
> 1007 68730  63934 uc010etm.3    chr12  71612488  71612788   301      *
> 1008 32071   7038 uc003ytw.3    chr12  71612488  71612788   301      *
> 1009 68728  63934 uc002qnd.3    chr14  24809972  24810272   301      *
> 1010 68729  63934 uc002qne.3    chr14  24809972  24810272   301      *
>
>
>
>
>   -- 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] Homo.sapiens_1.1.1
>   [2] GO.db_2.9.0
>   [3] OrganismDbi_1.2.0
>   [4] org.Hs.eg.db_2.9.0
>   [5] RSQLite_0.11.4
>   [6] DBI_0.2-7
>   [7] VariantAnnotation_1.6.6
>   [8] Rsamtools_1.12.3
>   [9] BSgenome.Hsapiens.UCSC.hg19_1.3.19
> [10] BSgenome_1.28.0
> [11] Biostrings_2.28.0
> [12] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2
> [13] GenomicFeatures_1.12.2
> [14] AnnotationDbi_1.22.6
> [15] Biobase_2.20.0
> [16] GenomicRanges_1.12.4
> [17] IRanges_1.18.1
> [18] BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>   [1] biomaRt_2.16.0     bitops_1.0-5       graph_1.38.2       RBGL_1.36.2
>   [5] RCurl_1.95-4.1     rtracklayer_1.20.2 stats4_3.0.1       tools_3.0.1
>   [9] XML_3.98-1.1       zlibbioc_1.6.0
>
> --
> Sent via the guest posting facility at bioconductor.org.