Copy Number Variation in the cn.mops Package
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@bioconductor-8383
Last seen 6.2 years ago

Hi all,
 

I'm trying to detect CNVs in different NGS samples for a single gene, so the the .bam files are not necessarily huge. I am, however, running into what *I think* is a syntax error below. Not quite sure what I'm doing wrong. Any input will be greatly appreciated.

Thanks.

OAO

> BAMFiles = list.files(pattern=".bam$")
> bamDataRanges = getReadCountsFromBAM(BAMFiles, sampleNames=paste("Sample",1:

3),WL = 5000, mode="paired")
Identified the following reference sequences:  chr7,chr20
Missing "refSeqName"! Selecting chr7 as reference sequence.
Using indexed BAM files.
Reading file: 001_sorted.bam
  chr7


Reading file: 002_sorted.bam
  chr7


Reading file: 003_sorted.bam
  chr7


Error in which(is.na(prov_ids) & .hasPrefix(seqlevels, prefix)) :
  error in evaluating the argument 'x' in selecting a method for function 'which': Error in nchar(prefix) :
  could not find symbol "keepNA" in environment of the generic function

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_xxx  LC_CTYPE=English_xxx  
[3] LC_MONETARY=English_xxx LC_NUMERIC=C                        
[5] LC_TIME=English_xxx   

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base    

other attached packages:
[1] cn.mops_1.14.0       GenomicRanges_1.20.5 GenomeInfoDb_1.4.1 
[4] IRanges_2.2.5        S4Vectors_0.6.1      Biobase_2.28.0     
[7] BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.14.0   XVector_0.8.0     Biostrings_2.36.1 Rsamtools_1.20.4
[5] bitops_1.0-6    
>

cn.mops cnv cnvtools • 1.4k views
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Entering edit mode
@gunter-klambauer-5426
Last seen 8 months ago
Austria

Hello OAO,

The function "getReadCountsFromBAM" is a wrapper for Rsamtools::countBam. I think the problem lies somewhere there.. can you give me the results of "traceback()" after the error occurs? Are you sure everything is ok with your BAM files?

 

Regards,

Günter

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@gunter-klambauer-5426
Last seen 8 months ago
Austria

Via email:

###############################################

Hi Gunter,
 

Ran 'traceback()':

> traceback()
13: which(is.na(prov_ids) & .hasPrefix(seqlevels, prefix))
12: assignProvIdsForSuperGroup(seqlevels, "CHR")
11: rankSeqlevels(x, X.is.sexchrom = X.is.sexchrom)
10: eval(expr, envir, enclos)
9: eval(quote(list(...)), env)
8: eval(quote(list(...)), env)
7: standardGeneric("order")
6: order(rankSeqlevels(x, X.is.sexchrom = X.is.sexchrom))
5: sortSeqlevels(seqlevels(x), X.is.sexchrom = X.is.sexchrom)
4: sortSeqlevels(seqlevels(x), X.is.sexchrom = X.is.sexchrom)
3: sortSeqlevels(gr)
2: sortSeqlevels(gr)
1: getReadCountsFromBAM(BAMFiles, sampleNames = paste("Sample",
       1:3), WL = 5000, mode = "paired", parallel = 0)
>

Regards,

Voke

###############################################

 

I think the problem occured somewhere in the logic of "Rsamtools" - could you please post this problem to the support page of "Rsamtools"?

 

Regards,

Günter

 

 

 

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This has come up several times recently. It seems very strange. The solution so far, e.g., at VariantAnnotation: scanVcfHeader() throws error about missing keepNA has been to update to R-3.2.1.

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Thanks for helping me out here, Martin!

Regards,

Günter

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Thank you Martin. That worked!

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Thanks Gunter.

-OAO

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Hello Voke,

Apologies - I pointed you towards "Rsamtools"... But the function "sortSeqlevels" comes from the package "GenomeInfoDb"..

 

Regards,

Günter

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Thanks Gunter. I have edited my subsequent post.

-OAO

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