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
>
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.
Thanks for helping me out here, Martin!
Regards,
Günter
Thank you Martin. That worked!
Thanks Gunter.
-OAO
Hello Voke,
Apologies - I pointed you towards "Rsamtools"... But the function "sortSeqlevels" comes from the package "GenomeInfoDb"..
Regards,
Günter
Thanks Gunter. I have edited my subsequent post.
-OAO