[BioC] read gz compressed wig files?

[Steve Lianoglou]

Hi,

On Thu, Mar 31, 2011 at 7:03 PM, Hamid Bolouri <hbolouri at gmail.com> wrote:
> 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

If you unzip the file and read it in "as normal", does it work differently?

-- 
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