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]]

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >