[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
--
Sent via the guest posting facility at bioconductor.org.
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