Entering edit mode
Hi,
I have a VCF with no info columns, and info(vcf) returns:
DataFrame with 0 rows and 0 columns
This should probably be N rows, 0 columns. That bug makes expand(vcf)
break
like this:
Error in icol[idx, ] :
selecting rows: subscript contains NAs or out of bounds indices
Thanks,
Michael
> sessionInfo()
R Under development (unstable) (2013-03-27 r62427)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] VariantTools_1.3.0 VariantAnnotation_1.5.45
Rsamtools_1.11.27
[4] Biostrings_2.27.13 GenomicRanges_1.11.42
IRanges_1.17.41
[7] BiocGenerics_0.5.6 rjson_0.2.12
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.21.16 Biobase_2.19.3 biomaRt_2.15.1
[4] bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5
[7] GenomicFeatures_1.11.16 gmapR_1.1.16 graph_1.37.7
[10] grid_3.1.0 lattice_0.20-15 Matrix_1.0-12
[13] RBGL_1.35.0 RCurl_1.95-4.1 RSQLite_0.11.2
[16] rtracklayer_1.19.11 stats4_3.1.0 tools_3.1.0
[19] XML_3.96-0.2 zlibbioc_1.5.0
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