Do you really just want to see the values, or is the goal to compute on
them? That AD field seems a bit strange, because the first sample is
missing values. By convention, the AD has values for the ref and alts,
across all of the samples.  In order to really work with these data, you'll
need to convert that list matrix to a cube with NAs as padding. I wouldn't
be able to suggest how without having my hands on the actual matrix.

If you really do just want to see them, you can do
unstrsplit(CharacterList(AD), ",") in devel, or use
rtracklayer:::pasteCollapse instead of unstrsplit in release. Then wrap
that result back into a matrix.



On Mon, Apr 7, 2014 at 10:53 PM, Lavinia Gordon
<Lavinia.Gordon@agrf.org.au>wrote:

> Dear All
>
> Using VariantAnnotation to parse a vcf file:
>
> ADvcf <- geno(vcf)$AD
>
> How can I access these values?
>
> ADvcf[1:2,1:2]
>             Sample1   Sample2
> chrM:72_T/C Integer,0 Integer,2
> chrM:73_G/A Integer,0 Integer,2
>
> as ideally I'd like something like:
> ADvcf[1:2,1:2]
>             Sample1   Sample2
> chrM:72_T/C      6,2          10,18
> chrM:73_G/A    5,40        0,23
>
> Thank you.
>
> Lavinia Gordon
> Bioinformatics Manager
>
> Australian Genome Research Facility Ltd
> The Walter and Eliza Hall Institute
> 1G Royal Parade
> Parkville VIC 3050
> Australia
>
> sessionInfo()
> R version 3.0.3 (2014-03-06)
> 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=en_US.UTF-8       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] VariantAnnotation_1.8.13 Rsamtools_1.14.3         Biostrings_2.30.1
> [4] GenomicRanges_1.14.4     XVector_0.2.0            IRanges_1.20.7
> [7] BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.24.0   Biobase_2.22.0         biomaRt_2.18.0
>  [4] bitops_1.0-6           BSgenome_1.30.0        DBI_0.2-7
>  [7] GenomicFeatures_1.14.5 RCurl_1.95-4.1         RSQLite_0.11.4
> [10] rtracklayer_1.22.7     stats4_3.0.3           tools_3.0.3
> [13] XML_3.98-1.1           zlibbioc_1.8.0
>
>         [[alternative HTML version deleted]]
>
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