[BioC] Snp matching

[Rhoda Kinsella]

Hi Mohamed,
I am glad that my suggestion has helped but i'm afraid I am not an  
expert bioconductor user. Perhaps someone else on this mailing list  
has experience with similar queries?
I hope you find an answer to your query,
Regards,
Rhoda


On 29 Sep 2009, at 13:59, Mohamed Lajnef wrote:

> Hi Rhoda,
>
> thank you for your answer! it works, but among my list of genes  i  
> can not find the gene SAM(sam-adenosylmethionine transporter)  when  
> i used org.Hs.egALIAS2EG mappings .
>
> library(org.Hs.eg.db)
> library("SNPlocs.Hsapiens.dbSNP.20080617")
> gene<-c("PPP3CC","DNMT1","SMS","SAM","MTHFR")
> egs <- unlist(mget(gene1, org.Hs.egALIAS2EG))
>
>
> *Error dans .checkKeys(value, Rkeys(x), x at ifnotfound) :
>   value for "SAM" not found*
>
> All suggestions are welcome!
>
> Thanks
>
>
> Best
>
>
> M
>
>
> Rhoda Kinsella a écrit :
>> Hi Mohamed,
>> I've just had a look at the Bioconductor Changelog (http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/biomaRt 
>> ) and there is an entry on 14th Jan 2009 that says:
>>
>> biomaRt
>> Removed getSNP, getHomolog, getAffyArrays as these functions are  
>> replaced by getBM and getLDS
>>
>>
>> So i guess you should try to use getBM or getLDS instead of getSNP.
>> Regards,
>> Rhoda
>>
>>
>> On 29 Sep 2009, at 08:47, Mohamed Lajnef wrote:
>>
>>> Dear All,
>>>
>>> I try to use biomart package to find the snps matching of some  
>>> genes:
>>> PPP3CC
>>> DNMT1
>>> SMS
>>> PPIEL
>>> SAM
>>> MTHFR
>>> snpmart = useMart("snp", dataset = "hsapiens_snp")  but getSnp  
>>> function does not work and i have this message
>>> Error:"Can not find function "getSNP", Can someone help me to  
>>> solve this problem?
>>> Regards
>>> M
>>>
>>>
>>> -- 
>>> Mohamed Lajnef
>>> INSERM Unité 955. 40 rue de Mesly. 94000 Créteil.
>>> Courriel : Mohamed.lajnef at inserm.fr tel. : 01 49 81 31 31 (poste  
>>> 18470)
>>> Sec : 01 49 81 32 90
>>> fax : 01 49 81 30 99
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>> Rhoda Kinsella Ph.D.
>> Ensembl Bioinformatician,
>> European Bioinformatics Institute (EMBL-EBI),
>> Wellcome Trust Genome Campus,
>> Hinxton
>> Cambridge CB10 1SD,
>> UK.
>>
>>
>
>
> -- 
> Mohamed Lajnef
> INSERM Unité 955. 40 rue de Mesly. 94000 Créteil.
> Courriel : Mohamed.lajnef at inserm.fr tel. : 01 49 81 31 31 (poste  
> 18470)
> Sec : 01 49 81 32 90
> fax : 01 49 81 30 99

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.