[BioC] Snp matching

[Mohamed Lajnef]

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
>> _______________________________________________
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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