[BioC] Wig files?

[Siefker, Ed B.]

Gladly. The Wig is available at:
https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/coad/gsc/hgsc.bcm.edu/illuminaga_dnaseq/mutations/hgsc.bcm.edu_COAD.IlluminaGA_DNASeq.Level_2.1.1.0/TCGA-A6-3807.wig.bz2

My R session looks like this:

>source("http://bioconductor.org/biocLite.R")
>biocLite("rtracklayer")
>library(rtracklayer)
>wigtest  <- import("TCGA-A6-3807.wig", asRangedData = FALSE)

That ran for about 4 hours but apparently completed.

> class(wigtest)
[1] "SimpleGenomicRangesList"
attr(,"package")
[1] "GenomicRanges"
> length(wigtest)
[1] 199482
> head(wigtest[[1]])
GRanges with 6 ranges and 1 elementMetadata col:
      seqnames         ranges strand |     score
         <Rle>      <IRanges>  <Rle> | <numeric>
  [1]     chr1 [20227, 20227]      * |         1
  [2]     chr1 [20228, 20228]      * |         1
  [3]     chr1 [20229, 20229]      * |         1
  [4]     chr1 [20230, 20230]      * |         1
  [5]     chr1 [20231, 20231]      * |         1
  [6]     chr1 [20232, 20232]      * |         1
  ---
  seqlengths:
   chr1
     NA

However the R process is now consuming 9.8 gigs of memory.
I am using a manually compiled version of R on RHEL6.
Here is my sessionInfo():

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] rtracklayer_1.16.2  GenomicRanges_1.8.7 IRanges_1.14.4     
[4] BiocGenerics_0.2.0  BiocInstaller_1.4.7

loaded via a namespace (and not attached):
[1] Biostrings_2.24.1 bitops_1.0-4.1    BSgenome_1.24.0   RCurl_1.91-1     
[5] Rsamtools_1.8.5   stats4_2.15.0     tools_2.15.0      XML_3.9-4        
[9] zlibbioc_1.2.0   

I think that's all the information I have that would be useful
to you.  Let me know if I forgot anything.  Thanks.
-Ed

________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] on behalf of Michael Lawrence [lawrence.michael at gene.com]
Sent: Thursday, July 12, 2012 7:00 PM
To: Ed Siefker
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Wig files?

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 at 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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