[BioC] VariantAnnotation package with snp location

[Fabrice Tourre]

Tim,

Thank you very much. It is really helpful to me. I learn a lot from your reply.

Best wishes,



On Fri, Feb 8, 2013 at 12:51 PM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> Minor derp:
>
> values(vars)[, c(1,2,3,5,6,7)] ## so that it fits in an email :-)
>
> ## was actually run as
>
> values(vars)[, c(1,5,6,7)]
>
> ## my bad
>
>
>
>
> On Fri, Feb 8, 2013 at 9:50 AM, Tim Triche, Jr. <tim.triche at gmail.com>
> wrote:
>>
>> suppose you have your SNPs in a data.frame named 'SNPs' with columns
>> 'chrom' and 'location', and suppose they're called against hg19.  Say,
>>
>> SNPs <- data.frame(chrom=c('chr1','chr9'), location=c(123, 456))
>>
>> ## To use locateVariants easily, you'll want to turn them into a GRanges.
>>
>> library(GenomicRanges)
>> SNPs.gr <- GRanges( seqnames=SNPs$chrom,
>>                                        IRanges(start=SNPs$location,
>> width=1) )
>> genome(SNPs.gr) <- 'hg19'  ## always record your genome, always always
>>
>> ## Then:
>>
>> library(Homo.sapiens)
>> library(VariantAnnotation)
>>
>> vars <- locateVariants(SNPs.gr,  ## the following is from Homo.sapiens
>>                                        TxDb.Hsapiens.UCSC.hg19.knownGene,
>>                                        AllVariants())
>>
>> values(vars)[, c(1,2,3,5,6,7)] ## so that it fits in an email :-)
>> ## DataFrame with 2 rows and 4 columns
>> ##    LOCATION      GENEID   PRECEDEID    FOLLOWID
>> ## 1 intergenic                  NA       79501              653635
>> ## 2 intergenic                  NA       81704            100287171
>>
>> ## As the above are both intergenic, you might like to know what they're
>> near:
>> ##
>> unlist(mget(vars$PRECEDEID, org.Hs.egSYMBOL)) ## from Homo.sapiens
>> ##  79501   81704
>> ##  "OR4F5" "DOCK8"
>>
>> unlist(mget(vars$FOLLOWID, org.Hs.egSYMBOL)) ## from Homo.sapiens
>> ##    653635 100287171
>> ##  "WASH7P"   "WASH1"
>>
>> Does this make sense?
>>
>> It is a tremendously useful package (thanks much to Valerie, Martin,
>> Michael and Stephanie).
>>
>>
>> On Fri, Feb 8, 2013 at 9:29 AM, Fabrice Tourre <fabrice.ciup at gmail.com>
>> wrote:
>>>
>>> Dear list,
>>>
>>> I am using VariantAnnotation package to annotated a list of snps. But
>>> I only have the snp coordinate information. It seems VariantAnnotation
>>> only works with VCF format. I am not family with VCF format.
>>>
>>> How can I use VariantAnnotation with my snp list? It is not vcf format.
>>>
>>>
>>> Thank you very much in advance.
>>>
>>> Best wishes,
>>>
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>>
>>
>>
>>
>> --
>> A model is a lie that helps you see the truth.
>>
>> Howard Skipper
>
>
>
>
> --
> A model is a lie that helps you see the truth.
>
> Howard Skipper