[BioC] Subset of samples with VariantAnnotation::readVcf

[Valerie Obenchain]

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
>
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