[BioC] biomaRt - retrieve chrom location

[Steffen Durinck]

Dear Joao,

Try:

a <- getGene(id = unique_UniGeneCluster[,1], type = "unigene", mart = ensembl)


Also if you are only interested in the chromosomal positions you might 
want to use the more general getBM function.
Your query would look like this:

a = 
getBM(c("unigene","ensembl_transcript_id","chromosome_name","start_position","end_position"),filters="unigene",values= 
unique_UniGeneCluster[,1] , mart=ensembl)

Best regards,
Steffen

João Fadista wrote:
> Dear list,
>  
> I would like to know how I can retrieve the chromosome position of each UniGene cluster id using biomaRt package. Here it is my script:
>  
>  > library(biomaRt)
>   
>> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
>>     
> Checking attributes and filters ... ok
>   
>> unique_UniGeneCluster <- read.csv(file="C:/CGH_experiment2/unique_UniGeneCluster.txt", header=F, sep = "\t")
>> a <- getGene(id = unique_UniGeneCluster, type = "unigene", mart = ensembl)
>> a
>>     
> NULL
>   
>> head(unique_UniGeneCluster)
>>     
>          V1
> 1  Hs.53454
> 2 Hs.433201
> 3 Hs.519601
> 4 Hs.100299
> 5 Hs.459088
> 6 Hs.514038
>   
>> class(unique_UniGeneCluster)
>>     
> [1] "data.frame"
>   
>> session.Info()
>>     
> Error: could not find function "session.Info"
>   
>> sessionInfo()
>>     
> R version 2.4.1 (2006-12-18) 
> i386-pc-mingw32 
>  
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>  
> attached base packages:
> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     
>  
> other attached packages:
>      sma    limma  biomaRt    RCurl      XML 
> "0.5.15" "2.9.17"  "1.8.2"  "0.8-0"  "1.6-0" 
>
>
>  
>
> Med venlig hilsen / Regards
>
> João Fadista
> Ph.d. studerende / Ph.d. student
>
>
>  	
>  	 AARHUS UNIVERSITET / UNIVERSITY OF AARHUS	
> Det Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences	
> Inst. for Genetik og Bioteknologi / Dept. of Genetics and Biotechnology	
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> DK-8830 Tjele	
>  	
> Tel:	 +45 8999 1900	
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> E-mail:	 Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk> 	
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-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
URL: http://home.ccr.cancer.gov/oncology/oncogenomics/

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