[BioC] copyCountSegments(fit) failed exomeCopy

[Michael Love]

hello Dan,

The issue appears to be some unsorted ranges in rdata, which are probably coming from overlapping regions in the target BED file from Agilent.  A solution is to first sort and reduce the original GRanges object 'target': 

target <- reduce(sort(target))

I should make subdivideGRanges do this automatically and I should check in the downstream functions that the ranges are in fact in order.

> as.data.frame(ranges(rdata["22"]))[4256:4259,]
     space    start      end width
4256    22 19951678 19951784   107
4257    22 19951785 19951891   107
4258    22 19951046 19951148   103
4259    22 19951149 19951252   104

best,

Mike

    Message: 35
    Date: Mon, 23 Apr 2012 19:45:32 +0000
    From: Dan Spiegelman <dan.spiegelman at crchum.qc.ca>
    To: <bioconductor at stat.math.ethz.ch>
    Subject: Re: [BioC] copyCountSegments(fit) failed exomeCopy
    Message-ID: <loom.20120423T214423-761 at post.gmane.org>
    Content-Type: text/plain; charset="utf-8"


    Hello,

    I am encountering a similar problem, though my data DOES have variants (i.e. is 
    not 100% normal state). 

    In setting up this analysis, I followed the procedure laid out in 
    http://www.bioconductor.org/packages/2.9/bioc/vignettes/exomeCopy/inst/doc/exome
    Copy.pdf virtually to the letter (except where my sample names and bamfile paths 
    are concerned).