hi,
there's a warning issued by GenomeInfoDb::keepStandardChromosomes()
because of multiple compatible sequence styles, that i guess it should
be corrected. this warning can be reproduced minimally as follows;
library(GenomicRanges)
library(GenomeInfoDb)
gr <- GRanges(seqnames="1", IRanges(1, 10))
gr <- keepStandardChromosomes(gr)
Warning message:
In if (!is.na(guess)) style <- unique(guess$style) else
return(dropSeqlevels(x, :
the condition has length > 1 and only the first element will be used
you can find the session info below. the specific line of code affected
on the lastest SVN version of GenomeInfoDb is:
keepStandardChromosomes <- function(x, species=NULL)
{
ori_seqlevels <- seqlevels(x)
if(!length(ori_seqlevels))
return(x)
## guess at style
guess <- .guessSpeciesStyle(ori_seqlevels)
if (!is.na(guess))
style <- unique(guess$style)
[...]
cheers,
robert.
ps: sessionInfo()
R Under development (unstable) (2016-05-04 r70581)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF8 LC_COLLATE=en_US.UTF8
[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
[7] LC_PAPER=en_US.UTF8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices
[6] utils datasets methods base
other attached packages:
[1] GenomicRanges_1.25.94 GenomeInfoDb_1.9.13
[3] IRanges_2.7.16 S4Vectors_0.11.17
[5] BiocGenerics_0.19.2 setwidth_1.0-4
[7] colorout_1.0-3
loaded via a namespace (and not attached):
[1] zlibbioc_1.19.0 XVector_0.13.7
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