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@love-5173
Last seen 10.2 years ago
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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