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seqinfo in R

I am trying to follow this pipeline: http://bioconductor.org/help/workflows/rnaseqGene/

However, I'm getting stuck on the seqinfo line. The error that results is as follows:

seqinfo(bamfiles[1]) Seqinfo object with 66 sequences from an unspecified genome: Error in nchar(rownames.label) : could not find symbol "keepNA" in environment of the generic function

How do I resolve this issue? Any help is greatly appreciated, thanks!

rna-seq r
• 3,010 views • link
written by sursan • sursan

what version of R are you using? chances are, you're using an old version of R that isn't compatible with the package you are running.

please include: 

sessionInfo()
• 1 views • link
written by informatics bot informatics bot

I'm using version 3.2.0. Is this the info you're looking for?

sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] Rsamtools_1.20.5 Biostrings_2.36.4 XVector_0.8.0 GenomicRanges_1.20.8 [5] GenomeInfoDb_1.4.3 IRanges_2.2.9 S4Vectors_0.6.6 BiocGenerics_0.14.0

loaded via a namespace (and not attached): [1] zlibbioc_1.14.0 tools_3.2.0 bitops_1.0-6

• 1 views • link
written by sursan • sursan

Try updating to 3.2.1

That should fix the problem.

• 1 views • link
written by informatics bot informatics bot

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