[BioC] stranded intronic variants with VariantAnnotation::locateVariants()
Valerie Obenchain
vobencha at fhcrc.org
Fri Oct 18 22:19:06 CEST 2013
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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