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

[Steve Lianoglou]

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