[BioC] Snp matching
Mohamed Lajnef
Mohamed.lajnef at inserm.fr
Tue Sep 29 14:59:56 CEST 2009
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
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