[BioC] GenomeinfoDB

Arora, Sonali sarora at fhcrc.org
Wed Jul 2 16:58:42 CEST 2014


Hi Isran

I have just added support for Mus musculus in version 1.1.10 of GenomeInfoDb

> library(GenomeInfoDb)
> names(genomeStyles())
 [1] "Arabidopsis_thaliana"     "Caenorhabditis_elegans"   "Cyanidioschyzon_merolae" 
 [4] "Drosophila_melanogaster"  "Homo_sapiens"             "Mus_musculus"            
 [7] "Oryza_sativa"             "Populus_trichocarpa"      "Saccharomyces_cerevisiae"
[10] "Zea_mays"                
> genomeStyles("Mus_musculus")
   circular  auto   sex NCBI  UCSC
1     FALSE  TRUE FALSE    1  chr1
2     FALSE  TRUE FALSE    2  chr2
3     FALSE  TRUE FALSE    3  chr3
4     FALSE  TRUE FALSE    4  chr4
5     FALSE  TRUE FALSE    5  chr5
6     FALSE  TRUE FALSE    6  chr6
7     FALSE  TRUE FALSE    7  chr7
8     FALSE  TRUE FALSE    8  chr8
9     FALSE  TRUE FALSE    9  chr9
10    FALSE  TRUE FALSE   10 chr10
11    FALSE  TRUE FALSE   11 chr11
12    FALSE  TRUE FALSE   12 chr12
13    FALSE  TRUE FALSE   13 chr13
14    FALSE  TRUE FALSE   14 chr14
15    FALSE  TRUE FALSE   15 chr15
16    FALSE  TRUE FALSE   16 chr16
17    FALSE  TRUE FALSE   17 chr17
18    FALSE  TRUE FALSE   18 chr18
19    FALSE  TRUE FALSE   19 chr19
20    FALSE FALSE  TRUE    X  chrX
21    FALSE FALSE  TRUE    Y  chrY
22     TRUE FALSE FALSE   MT  chrM

Hope that helps!

You can grab it from svn immediately or from biocLite() tomorrow. 



-- 
Sonali Arora

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: sarora at fhcrc.org
Phone:  (206) 667-4746
Fax:    (206) 667-4746 

----- Original Message -----
From: "Irsan [guest]" <guest at bioconductor.org>
To: bioconductor at r-project.org, "ei kooi" <ei.kooi at vumc.nl>
Sent: Wednesday, July 2, 2014 7:08:10 AM
Subject: [BioC] GenomeinfoDB

Currently, the GenomeInfoDb does not support Mus musculus. How can I make it available for my local installation? It would be great if it somebody can make it available in the GenomeInfoDb package. I prepared the genes_species.txt file:

circular	auto	sex	NCBI	UCSC
F	T	F	1	chr1
F	T	F	2	chr2
F	T	F	3	chr3
F	T	F	4	chr4
F	T	F	5	chr5
F	T	F	6	chr6
F	T	F	7	chr7
F	T	F	8	chr8
F	T	F	9	chr9
F	T	F	10	chr10
F	T	F	11	chr11
F	T	F	12	chr12
F	T	F	13	chr13
F	T	F	14	chr14
F	T	F	15	chr15
F	T	F	16	chr16
F	T	F	17	chr17
F	T	F	18	chr18
F	T	F	19	chr19
F	F	T	X	chrX
F	F	T	Y	chrY
T	F	F	MT	chrM

 -- output of sessionInfo(): 

R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base 

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