[BioC] copyCountSegments(fit) failed exomeCopy

[love]

Hi John,

This appears to be a bug for fitted objects which have no predicted
variants (as the show command gives "percent normal state: 100%").  I will
fix it.  

best,

Mike 

> 
> ----- Forwarded Message -----
> From: John linux-user <johnlinuxuser at yahoo.com>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org> 
> Sent: Sunday, March 18, 2012 1:54 PM
> Subject: [BioC] copyCountSegments(fit) failed exomeCopy
>  
> 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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> 
> 
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