I can confirm reducing the target removes that error.
I simply added in my script

target <- reduce(target)
target.sub <- subdivideGRanges(target)

thanks very much for your help,
Francesco



On 7 Aug 2012, at 15:51, Michael Love <love@molgen.mpg.de<mailto:love@molgen.mpg.de>> wrote:

On 08/07/12 15:41, Lescai, Francesco wrote:
Thanks Mike,
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?

thanks,
Francesco


On 6 Aug 2012, at 23:46, Mike Love <love@molgen.mpg.de<mailto:love@molgen.mpg.de>> wrote:

On Tue, Aug 7, 2012 at 12:11 AM, Lescai, Francesco <f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk>> wrote:
Hi there,
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 formatted correctly

> fit.list[[1]][1]
$`1`

ExomeCopy object
sample name: UCLG_502_ATCACG_L003
percent normal state: 79.87%

> summary(fit.list$UCLG_502_ATCACG_L003$`1`)
   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


Hi Francesco,

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 you try:

all.equal(target, reduce(target))

If these are in fact equal, you can send me the fit.list object and I can try to debug.

best,

Mike


Hi Francesco,

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.

Mike

---------------------------------------------------------------------------------
Francesco Lescai, PhD, EDBT
Senior Research Associate in Genome Analysis
University College London
Faculty of Population Health Sciences
Dept. Genes, Development & Disease
ICH - Molecular Medicine Unit, GOSgene team
30 Guilford Street
WC1N 1EH London UK

email: f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
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