Entering edit mode
Richard Pearson
▴
80
@richard-pearson-5255
Last seen 10.1 years ago
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