[BioC] How to retrieve locusID from ensembl using biomaRt package version 1.6.0

[Wolfgang Huber]

Dear Shiliang,

please send us an R script that allows us to reproduce your error.
"Wrong information" is too unconcrete, I am afraid to say.

Also, please use the most recent version biomaRt 1.7.3 from
http://bioconductor.org/packages/1.9/bioc

Best wishes
 Wolfgang

-- 
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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

swang wrote:
> Dear list:
> 
> I am a newbie for R language, I just wonder that how to use biomaRt to
> retrieve all locusIDs between two SNPs from ensembl using biomaRt package.
> I tried to use getBM(), getSequence(), getGene(), but it always give me
> wrong information.
> 
> also I have question about enviroment that I scratched the statement from
> review of biomaRt 1.6.0 version into R(version 2.3.1)
> 
>> mart = useMart("snp", dataset = "hsapiens_snp")
> Checking attributes and filters ... ok
>>
>> getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart)
> Error in getBM(attributes = attributes, filters = c("chr_name", snpstart,  :
> 
>         filter: snp_chrom_start not found, please use the function
> 'listFilters' to get valid filter names
>> getSequence(chromsome=5, start=240457, end=
> 356304,type="ensembl",seqType="cdna",mart=mart)
> Error in getSequence(chromsome = 5, start = 240457, end = 356304, type =
> "ensembl",  :
>         unused argument(s) (chromsome ...)
> Is there anybody who can help me out of this situation.
> 
> Thanks
> 
> Shiliang
>