[BioC] read gz compressed wig files?

[Steve Lianoglou]

Sorry, forgot to add that these import.wig and import.bw are in the
rtracklayer package.

On Thu, Mar 31, 2011 at 3:04 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> On Mon, Mar 28, 2011 at 5:32 PM, Hamid Bolouri <hbolouri at gmail.com> wrote:
>> hi; Is there a way to read gz compressed wiggle files (.wig.gz)
>> without decompressing them first? I couldn't find anything online.
>>
>> Example files:
>>
>> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeRegMarkEnhH3k27ac/
>
> Maybe the import.wig (or import.bw if you've got bigwig files).
>
> That function take in a `con` (connection) object, perhaps you can
> make a "connection" to your wig.gz file via `gzopen()` and pass the
> result into the import.wig, ie:
>
> R> import.wig(gzopen('/path/to/*.wig.gz'))
>
> I actually haven't tried it, but I reckon it could work.
>
> -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
>



-- 
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