Valerie Obenchain | 7 Apr 20:55 2013

Re: expand() vcf with no info columns

In 1.7.3, info(vcf) now returns an empty DataFrame with N rows, 0 
columns. I added a dimension check in the validity such that 
nrow(info(vcf)) must match the length(rowData(vcf)).

expand() was also breaking with an empty geno(vcf) so that is fixed now too.

Thanks for reporting this.

Val

On 04/04/13 13:49, Michael Lawrence wrote:
> 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
>
> 	[[alternative HTML version deleted]]
>
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