GenomeinfoDB
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Last seen 7.1 years ago
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.
Mus musculus GenomeInfoDb Mus musculus GenomeInfoDb • 1.0k views
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Sonali Arora ▴ 380
@sonali-arora-6563
Last seen 5.5 years ago
United States
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@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. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Irsan, Sonali, Just a FYI that the purpose of the small db included in GenomeInfoDb is to support seqlevelsStyle() and seqlevelsStyle() should work properly on your Mouse data because the chromosome names for Mouse are a subset of the chromosome names for Human. Maybe we should clarify this in the documentation. Cheers, H. On 07/02/2014 07:58 AM, Arora, Sonali wrote: > 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. > > > -- Hervé Pagès 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: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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