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

[Robert Castelo]

Great! thanks a lot Valerie!!

robert.

On 10/18/13 10:19 PM, Valerie Obenchain wrote:
> 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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>