[BioC] VariantAnnotation: fine define Locating variants in and around genes

[Fabrice Tourre]

Valerie,

Thank you for your reply.

Is there a function in VariantAnnotation to know whether a snp is
within transcription region but outside coding region? Or is it in
first exon/intron?

On Thu, Jan 31, 2013 at 4:30 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:
> Hi Fabrice,
>
> To identify snps (or any ranges) in introns only, use IntronVariants() as
> the 'region' argument. The CodingVariants are the exon regions. If you want
> all regions except coding, I would suggest using AllVariants().
>
> This output is from the man page example. The 'loc_coding' name is
> misleading since AllVariants were use as 'region'. I have changed it to
> 'loc_all' in the devel branch.
>
>> loc_coding <- locateVariants(vcf_adj, txdb, AllVariants())
>> loc_coding
> GRanges with 16 ranges and 7 metadata columns:
>              seqnames               ranges strand |   LOCATION   QUERYID
>                 <Rle>            <IRanges>  <Rle> |   <factor> <integer>
>                  chr1 [   13220,    13220]      * |     intron         1
>                  chr1 [   13220,    13220]      * | spliceSite         1
>                  chr1 [   13220,    13220]      * |     intron         1
>                  chr1 [   13220,    13220]      * |     intron         1
>                  chr1 [   13220,    13220]      * | spliceSite         1
> ...
> ...
>
> This example has variants in splice sites, introns, coding and intergenic
> regions.
>
>> tbl <- table(loc_coding$LOCATION)
>> tbl[tbl > 0]
>
> spliceSite     intron     coding intergenic
>          2          7          2          5
>
> The result can be subset on LOCATION for the region of interest. The QUERYID
> column maps back to the row number in the original 'query' argument to
> locateVariants().
>
> introns <- loc_coding[loc_coding$LOCATION == "intron", ]
>> head(introns, 3)
> GRanges with 3 ranges and 7 metadata columns:
>    seqnames         ranges strand | LOCATION   QUERYID      TXID
>       <Rle>      <IRanges>  <Rle> | <factor> <integer> <integer>
>        chr1 [13220, 13220]      * |   intron         1         1
>        chr1 [13220, 13220]      * |   intron         1         2
>        chr1 [13220, 13220]      * |   intron         1         3
>
>
> Valerie
>
>
>
> On 01/31/2013 12:34 PM, Fabrice Tourre wrote:
>>
>> Dear list,
>>
>> I am using VariantAnnotation to Locate variants in and around genes.
>>
>> In VariantAnnotation, the region is defined as: Coding Variants,
>> IntronVariants, FiveUTRVariants, ThreeUTRVariants, IntergenicVariants,
>> SpliceSiteVariants or PromoterVariants.
>>
>> If it possible to know whether a snp is in exon/intron within
>> transcription region but outside coding region?
>>
>> Thanks.
>>
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>