[BioC] Snp matching

[Mohamed Lajnef]

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

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.
>>>
>>> _______________________________________________
>>> 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
>>
>> _______________________________________________
>> 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
>
>


-- 
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