[BioC] GenomeinfoDB

[Hervé Pagès]

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
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