[BioC] Attribute in snp mart to get SNP function (e.g. synonymous, nonsynonymous) ?

[Valerie Obenchain]

On 11/14/2011 12:16 AM, Xavier de Pedro wrote:
> As far as I remember, only available since R 2.14.
> Cheers
> Xavier
>

Yes, that is correct. You'll need R-2.14 for VariantAnnotation.

To find the locations of your variant with biomaRt you could try 
'consequence_type_tv' as the attribute then filter on the value you want 
with 'consequence_type'.

## Here we select a group of snps from chr8:
snps_all<- getBM(c('refsnp_id','allele','chrom_start','chrom_strand', 
'consequence_type_tv', 'set_description', 'set_name'),
                          filters = 
c('chr_name','chrom_start','chrom_end'),
                          values = list(8,148350,158612),
                          mart = snpmart)

## List the possible values for 'consequence_type_tv':
 > unique(snps_all$consequence_type_tv)
  [1] "INTRONIC"
  [2] "DOWNSTREAM"
  [3] "SYNONYMOUS_CODING"
  [4] "WITHIN_NON_CODING_GENE"
  [5] "NON_SYNONYMOUS_CODING"
  [6] "UPSTREAM"
  [7] "WITHIN_NON_CODING_GENE&INTRONIC&SPLICE_SITE"
  [8] "WITHIN_NON_CODING_GENE&INTRONIC"
  [9] "WITHIN_NON_CODING_GENE&SPLICE_SITE"
[10] ""

## Select only nonsynonymous coding snps:
snps_nsc <- getBM(c('refsnp_id','allele','chrom_start','chrom_strand', 
'consequence_type_tv', 'set_description', 'set_name'),
                          filters = 
c('chr_name','chrom_start','chrom_end', 'consequence_type'),
                          values = list(8,148350,158612, 
'NON_SYNONYMOUS_CODING'),
                          mart = snpmart)

Valerie
> On 11/11/11 18:16, Adriana Munoz wrote:
>> Hi Valerie,
>>
>> Thanks for the information.  I used the filter you mentioned and it 
>> works.
>>   I'd like to try the Variant Annotation package that you mentioned to
>> get where my variant is located (coding, non-coding, utr, etc.) , 
>> too, but
>> I got the following error message in my Mac:
>> "Warning message:
>> In getDependencies(pkgs, dependencies, available, lib) :
>>    package ‘VariantAnnotation’ is not available (for R version 2.13.2)"
>>
>> Then, I tried loading the package in Windows that has R version 
>> 2.12., but
>> I  the following error message:
>> "Warning message:
>> In getDependencies(pkgs, dependencies, available, lib) :
>>    package ‘VariantAnnotation’ is not available"
>>
>> May I ask you if you know by chance  what version of R you were 
>> running for
>> the Variant Annotation package? or do you know of any attributes and
>> filters in Biomart to get where my variant is located (coding, 
>> non-coding,
>> utr, etc.)?
>>
>> Thanks,
>>
>> Adriana
>>
>> On Tue, Nov 8, 2011 at 7:37 PM, Valerie 
>> Obenchain<vobencha at fhcrc.org>wrote:
>>
>>> Hi Adriana,
>>>
>>> I believe the filter you want is consequence_type. Take a look at the
>>> filters available to you with,
>>>
>>>     listFilters(snpmart)
>>>
>>> You may also want to take a look at the VariantAnnotation package. 
>>> There
>>> are functions
>>>
>>>     ?locateVariants
>>>     ?predictCoding
>>>
>>> that can tell you where your variant is located (coding, non-coding, 
>>> utr,
>>> etc.) and provide the amino acid coding change is for the 
>>> non-synonymous
>>> variants. Recently SIFT and PolyPhen scores have been made available
>>> through db packages
>>> SIFT.Hsapiens.dbSNP132 and PolyPhen.Hsapiens.dbSNP131.
>>>
>>> Valerie
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 11/02/2011 07:33 AM, Adriana Munoz wrote:
>>>
>>>>> Hello,
>>>>>
>>>>> I'd like to ask you if there is an attribute to extract SNP function
>>>>> information from variation datasets in biomaRt such as synonymous,
>>>>> nonsynonymous, etc and
>>>>>
>>>>> a related filter.
>>>>>
>>>>> I'm using the following rcode:
>>>>>
>>>> snpmart = useMart("snp", dataset="hsapiens_snp")
>>>>
>>>>   Any help will be appreciated.
>>>>> Thanks,
>>>>>
>>>>> Adriana
>>>>>
>>>>>
>>>>>          [[alternative HTML version deleted]]
>>>>>
>