[BioC] Snp matching

[Hotz, Hans-Rudolf]

Hi Mohamed


I don't think it is a Bioconductor issue anymore...are you sure about the
gene name "SAM"? 

I am just guessing: How about "SAMC" or "SLC25A26"


Hans




On 9/29/09 3:11 PM, "Rhoda Kinsella" <rhoda at ebi.ac.uk> wrote:

> 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
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>> 
>>> 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.
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor