[BioC] Snp matching

[Martin Morgan]

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.
>>
>> _______________________________________________
>> 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
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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