Something is probably going wrong. Would you mind pointing me to this WIG
file, if it's something public?

Also, you'll find things to be a lot more efficient if you convert to
BigWig with wigToBigWig() and then import that.

Thanks,
Michael

On Thu, Jul 12, 2012 at 1:14 PM, Ed Siefker <ebs15242@gmail.com> wrote:

> What do I use to handle .wig files in a fast and convenient manner?
>
> I have a bunch of .wig files from the TCGA.  All I want to know is
> if a single position was sufficiently covered by the sequencer to
> call a mutation.  This is represented by a '1' at the appropriate
> line in the file.   Insufficient coverage is represented by a '0'
> or the lack of any lines corresponding to those coordinates.
>
> 'rtracklayer' seems to be the package people use to handle
> .wig files.   So I started R, installed 'rtracklayer' and executed:
> wigtest  <- import("TCGA-A6-3807.wig", asRangedData = FALSE)
> as indicated in the documentation.
>
> So far, it's been about 3 hours of maxed out CPU.  What is
> 'rtracklayer' doing?  Sure, it's a 91mb .wig, but I can grep
> the thing in less than 1s. Is this expected behavior?  Should
> I be going about this in a different way?
>
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