[BioC] Printing Alt alleles using VariantAnnotation

[James W. MacDonald]

Hi Mark,

On 9/28/2012 6:06 AM, Mark Dunning wrote:
> Hi all,
>
> I am doing some processing of vcf files using the VariantAnnotation
> package, and eventually I want to write out a table that I can use the
> annovar annotation package tool on
> (http://www.openbioinformatics.org/annovar/). The table needs to be in
> the form
>
> CHR, Start, end, Ref, Alt
>
> e.g.
>
> 1 55 55 T G
> 1 2646 2646 G A
>
> I'm fine extracting the chromosome, start and end. To get the
> referrence alleles I do.
>
>> Ref<- as.data.frame(values(ref(vcf))[["REF"]])[,1]
> But the Alt allele is a bit more complicated. If I do something like;
>
>> alternate = as.data.frame(unlist(values(fixed(vcf))[["ALT"]]))[,1]

How about

alternate <- sapply(values(fixed(vcf))[["ALT"]], paste, collapse = ",")

Best,

Jim


> The number of rows could be greater than the number of variants in the
> vcf file, especially for indels where more than one alternate allele
> could be found. I can no longer easily construct the data frame.
>
> Is there an easy way to write all alternate alleles for the same
> position in a comma-separated string so that entries in the table
> could be in the form
>
> 1 55 55 T G,C
> (e,g,  G and C alternate alleles were found for the SNP at position
> chromosome 1: 55-55)
>
>
> Regards,
>
> Mark
>
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> 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=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] VariantAnnotation_1.2.11 Rsamtools_1.8.6          Biostrings_2.24.1
> [4] ggplot2_0.9.2.1          GenomicRanges_1.8.13     IRanges_1.14.4
> [7] BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.18.3  Biobase_2.16.0        biomaRt_2.12.0
>   [4] bitops_1.0-4.1        BSgenome_1.24.0       colorspace_1.1-1
>   [7] DBI_0.2-5             dichromat_1.2-4       digest_0.5.2
> [10] GenomicFeatures_1.8.3 grid_2.15.1           gtable_0.1.1
> [13] labeling_0.1          lattice_0.20-10       MASS_7.3-21
> [16] Matrix_1.0-9          memoise_0.1           munsell_0.4
> [19] plyr_1.7.1            proto_0.3-9.2         RColorBrewer_1.0-5
> [22] RCurl_1.91-1          reshape2_1.2.1        RSQLite_0.11.2
> [25] rtracklayer_1.16.3    scales_0.2.2          snpStats_1.6.0
> [28] splines_2.15.1        stats4_2.15.1         stringr_0.6.1
> [31] survival_2.36-14      tools_2.15.1          XML_3.9-4
> [34] zlibbioc_1.2.0
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099