[BioC] biomaRt - retrieve chrom location

[James W. MacDonald]

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")

You probably want to use scan() here instead, so you end up with a 
vector of characters rather than a data.frame of (probably) factors.

Alternatively you could unlist() and as.character() your data.frame, but 
that's sort of a lot of work to undo what you didn't need to do in the 
first place ;-D

Best,

Jim


>>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	
>  	
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> E-mail:	 Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk> 	
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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