Hi Is it possible to read in data on a subset of samples with readVcf? The only way I've found of doing this is to read in data on all samples, then subset, but it would be much more efficient for me to read in data only for my samples of interest. Apologies if I've missed something obvious. Richard > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] VariantAnnotation_1.2.6 Rsamtools_1.8.4 Biostrings_2.24.1 GenomicRanges_1.8.3 IRanges_1.14.2 BiocGenerics_0.2.0 malariagen_0.0.1 BiocInstaller_1.4.3 loaded via a namespace (and not attached): [1] AnnotationDbi_1.18.0 Biobase_2.16.0 biomaRt_2.12.0 bitops_1.0-4.1 BSgenome_1.24.0 DBI_0.2-5 GenomicFeatures_1.8.1 grid_2.15.0 lattice_0.20-6 Matrix_1.0-6 [11] RCurl_1.91-1 RSQLite_0.11.1 rtracklayer_1.16.1 snpStats_1.6.0 splines_2.15.0 stats4_2.15.0 survival_2.36-14 tools_2.15.0 XML_3.9-4 zlibbioc_1.2.0

Hi Richard, No, we don't currently have a way to read in select samples. With ScanVcfParam() you can specify subsets of ranges or specific info and geno fields but not subjects. Maybe something for the TODO list if enough people are interested. Valerie On 04/27/2012 08:33 AM, Richard Pearson wrote: > Hi > > Is it possible to read in data on a subset of samples with readVcf? > The only way I've found of doing this is to read in data on all > samples, then subset, but it would be much more efficient for me to > read in data only for my samples of interest. > > Apologies if I've missed something obvious. > > Richard > > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] VariantAnnotation_1.2.6 Rsamtools_1.8.4 > Biostrings_2.24.1 GenomicRanges_1.8.3 > IRanges_1.14.2 BiocGenerics_0.2.0 > malariagen_0.0.1 BiocInstaller_1.4.3 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.18.0 Biobase_2.16.0 biomaRt_2.12.0 > bitops_1.0-4.1 BSgenome_1.24.0 DBI_0.2-5 > GenomicFeatures_1.8.1 grid_2.15.0 lattice_0.20-6 > Matrix_1.0-6 > [11] RCurl_1.91-1 RSQLite_0.11.1 rtracklayer_1.16.1 > snpStats_1.6.0 splines_2.15.0 stats4_2.15.0 > survival_2.36-14 tools_2.15.0 XML_3.9-4 > zlibbioc_1.2.0 > > _______________________________________________ > 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