[BioC] read gz compressed wig files?

[Hamid Bolouri]

Thanks Steve;

> import.wig(gzopen('C:\\...pathto...\\wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz'))
Error in import.wig(gzopen("C:\\Users\\hbolouri\\Desktop\\ENCODE_data\\wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz"))
:
  error in evaluating the argument 'con' in selecting a method for
function 'import.wig'

> traceback()
1: import.wig(gzopen("C:\\...\\wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz"))


using gzfile instead of gzopen avoids the error message, but seems to
produce an empty object
> import.wig(gzfile('C:\\...pathto...\\wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz'))
RangedDataList of length 0

> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United
States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] IRanges_1.8.8      rtracklayer_1.10.6 RCurl_1.5-0.1      bitops_1.0-4.1

loaded via a namespace (and not attached):
[1] Biobase_2.10.0      Biostrings_2.18.2   BSgenome_1.18.3
GenomicRanges_1.2.3 tools_2.12.1        XML_3.2-0.2
>

Thanks again.

Hamid


On Thu, Mar 31, 2011 at 12:04 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> 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
>



-- 
http://labs.fhcrc.org/bolouri