[BioC] stranded intronic variants with VariantAnnotation::locateVariants()

[Valerie Obenchain]

Hi Robert,

Yes, I can add that. I'll let you know when it's done.

Valerie

On 10/17/2013 04:01 AM, Robert Castelo wrote:
> hi,
>
> i have the following feature request for the VariantAnnotation package.
>
> currently, the function predictCoding() annotates the strand of variants
> within exons according to a given gene annotation. would it be possible
> that the function locateVariants() in the VariantAnnotation package
> annotates the strand for intronic variants?
>
> introns are non-coding, and therefore, not annotated with
> predictCoding(), but are stranded (GT-AG).
>
> here goes a code snippet that illustrates what i'm talking about
> (adapted from the vignette):
>
> =================
> library(VariantAnnotation)
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>
> fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> vcf <- readVcf(fl, "hg19")
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> seqlevels(vcf) <- "chr22"
> rd <- rowData(vcf)
> loc <- locateVariants(rd, txdb, IntronVariants())
>
> head(loc, n=3)
> GRanges with 3 ranges and 7 metadata columns:
>        seqnames               ranges strand | LOCATION   QUERYID
> TXID     CDSID      GENEID
>           <Rle>            <IRanges>  <Rle> | <factor> <integer>
> <integer> <integer> <character>
>    [1]    chr22 [50300078, 50300078]      * |   intron         1
> 75253      <NA>       79087
>    [2]    chr22 [50300086, 50300086]      * |   intron         2
> 75253      <NA>       79087
>    [3]    chr22 [50300101, 50300101]      * |   intron         3
> 75253      <NA>       79087
>              PRECEDEID        FOLLOWID
>        <CharacterList> <CharacterList>
>    [1]
>    [2]
>    [3]
>    ---
>    seqlengths:
>     chr22
>        NA
> =================
>
> i.e., the strand column is set to * for the intronic variants. it's ok
> if this new feature would be added to the devel version, as happens
> normally with new features.
>
>
> thanks!
> robert.
> ps: sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets methods
> [8] base
>
> other attached packages:
>   [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
>   [2] GenomicFeatures_1.14.0
>   [3] AnnotationDbi_1.24.0
>   [4] Biobase_2.22.0
>   [5] VariantAnnotation_1.8.0
>   [6] Rsamtools_1.14.1
>   [7] Biostrings_2.30.0
>   [8] GenomicRanges_1.14.1
>   [9] XVector_0.2.0
> [10] IRanges_1.20.0
> [11] BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
>   [1] biomaRt_2.18.0     bitops_1.0-6       BSgenome_1.30.0 DBI_0.2-7
>   [5] RCurl_1.95-4.1     RSQLite_0.11.4     rtracklayer_1.22.0 stats4_3.0.2
>   [9] tools_3.0.2        XML_3.95-0.2       zlibbioc_1.8.0
>
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