[BioC] error in exomeCopy - IRanges?
love at molgen.mpg.de
Tue Aug 7 16:51:31 CEST 2012
On 08/07/12 15:41, Lescai, Francesco wrote:
that seems exactly the case.
Does it mean I have to re-run both the reads counting and computation?
or can I fix it somehow?
On 6 Aug 2012, at 23:46, Mike Love <love at molgen.mpg.de> wrote:
On Tue, Aug 7, 2012 at 12:11 AM, Lescai,
Francesco <f.lescai at ucl.ac.uk> wrote:
I'm having an error in exomeCopy when I count the CNVs.
No previous error in any of the other steps illustrated in the vignette
the computation of the fit list didn't give any warning and it seems to be
sample name: UCLG_502_ATCACG_L003
percent normal state: 79.87%
Length Class Mode
1 ExomeCopy S4
but then I get
> compiled.segments <- compileCopyCountSegments(fit.list)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
solving row 1: negative widths are not allowed
I have seen this error before when the target GRanges has duplicate or
unsorted regions, and fixed this in the devel branch. You could try to
reduce the target GRanges first, before counting sample read counts. Could
If these are in fact equal, you can send me the fit.list object and I can
try to debug.
Sorry I should have written:
all.equal(target, reduce(target, min.gapwidth=0))
...as adjacent ranges are fine.
It is probably easier to re-run counting after reducing the target with
min.gapwidth=0. There could be complicated overlapping ranges generated if
you have overlapping but not identical regions in the original target file.
1. mailto:love at molgen.mpg.de
2. mailto:f.lescai at ucl.ac.uk
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