Hello

I tried to the copyCountSegments from exomeCopy, but it failed as shown below. It complained negative width, but I table the width value, and have never found any negative value in width column for range objects. Could any one give some suggestions? Thanks.

John


> fit <- exomeCopy(exomecounts["chr1"],sample.name="HGPIPE_6159",
+                    X.names=c("bg","GC","GC.sq","width"),S=0:6,d=2)
>   show(fit)

ExomeCopy object
type: exomeCopy
percent normal state: 100%
> copyCountSegments(fit)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 1: negative widths are not allowed

> sessionInfo()
R version 2.14.2 (2012-02-29)
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] exomeCopy_1.0.2     Rsamtools_1.6.3     Biostrings_2.22.0  
[4] GenomicRanges_1.6.7 IRanges_1.12.6      foreign_0.8-49     

loaded via a namespace (and not attached):
[1] bitops_1.0-4.1     BSgenome_1.22.0    RCurl_1.91-1       rtracklayer_1.14.4
[5] tools_2.14.2       XML_3.9-4          zlibbioc_1.0.1    
> 
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