[BioC] Snp matching

[Martin Morgan]

Mohamed Lajnef wrote:
> Dear  Martin & Hans,
> 
> gene not gene1 sorry for the mistake! yes i  am sure about this gene  
> (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=sam),
> 
> thank you again for your help

hmm, but these aren't from H. sapiens, and you're looking in the 
org.Hs.* database. Martin

> 
> M
> Martin Morgan a écrit :
>> Hotz, Hans-Rudolf wrote:
>>> 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))
>>
>> note 'gene1' instead of 'gene'
>>
>> it might be helpful to
>>
>> ids = ls(org.Hs.egALIAS2EG)
>> ids[grepl("SAM", ids)]
>>
>> or
>>
>> nms = ls(revmap(org.Hs.egGENENAME))
>> nms[grepl("adenosylmethionine", nms)]
>>
>> Martin
>>
>>>>>
>>>>>
>>>>> *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.
>>>>
>>>> _______________________________________________
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>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>> _______________________________________________
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>>
>>
> 
> 


-- 
Martin Morgan
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