[BioC] How can I obtain gene name from chromosome location?

[Tim Triche, Jr.]

The original poster did not specify whether these are promoter regions
or genic regions; if they are the former, flank() will be useful.


On Mon, Jul 9, 2012 at 12:43 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi Seungyeul,
>
> On Mon, Jul 9, 2012 at 3:28 PM, Yoo, Seungyeul <seungyeul.yoo at mssm.edu> wrote:
>> Hi all,
>>
>> I'm working on DNA-methylation data of Lung Genomes.
>>
>> I'm using CHARM packages for the analysis of differentially methylated regions.
>>
>> I can have a list of chromosomal locations indicating genes but I don't know how I map this location into specific gene names.
>>
>>> head(pns)
>> [1] "chr19:4205395-4220723"   "chr16:73793547-73835933"
>> [3] "chr22:18115791-18146966" "chr19:60540822-60563218"
>> [5] "chr16:14630202-14638324" "chr19:49197954-49200178"
>>
>> Because I also have gene expression dataset, I want to integrate dna methylation data so obtaining genename is very critical.
>>
>> Please let me have any advices.
>
> I'll just point you towards the way, and leave the (important) task of
> learning how to use these packages up to you (or another poster who
> feels that given you the exact commands is the best way to help you
> ;-)
>
> (1) Use the GenomicFeatures package to build a TranscriptDb for your
> organism and annotation  source of choice (refseq, ensembl, ucsc known
> genes):
>
> http://bioconductor.org/packages/2.10/bioc/html/GenomicFeatures.html
>
> (2) Represent your ranges (chr22:XXX-YYY) as a GenomicRanges object:
>
> http://bioconductor.org/packages/2.10/bioc/html/GenomicRanges.html
>
> (3) Extract the "transcripts" from your TranscriptDb object using the
> `transcripts` function
>
> (4) Use findOverlaps and friends (eg. subsetByOverlaps) to find which
> transcripts overlap which transcripts.
>
> The GenomicFeatures, GenomicRanges, and (if you really want to master
> your craft) IRanges packages each have pretty extensive documentation
> in terms of vignettes and API documentation that are worth your time
> to read -- once you do so, using those packages to perform the tasks
> outlined above will be rather straightforward.
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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A model is a lie that helps you see the truth.

Howard Skipper