Looks like a useful function. Someone should optimize it though. On Tue, Apr 8, 2014 at 8:52 AM, Stephanie M. Gogarten < sdmorris@u.washington.edu> wrote: > > > On 4/8/14 4:51 AM, Michael Lawrence wrote: > >> 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. >> > > VariantAnnotation has an internal function .matrixOfListsToArray that does > exactly this. Maybe it should be exported? > > > >> 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]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> [[alternative HTML version deleted]]