Entering edit mode
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
Calls: compileCopyCountSegments ... RangedData -> is -> IRanges ->
solveUserSEW0 -> .Call2 -> .Call
Execution halted
any idea is much appreciated.
thanks,
Francesco
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
[3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
[5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] exomeCopy_1.2.0 Rsamtools_1.8.5 Biostrings_2.24.1
[4] GenomicRanges_1.8.7 IRanges_1.14.4 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] bitops_1.0-4.1 stats4_2.15.0 zlibbioc_1.2.0