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    
>

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

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