[BioC] Biobase use problem

[Martin Morgan]

On 09/17/2011 01:38 PM, Ram H. Sharma wrote:
> I tried to install and use BSgenome, but I have problem in reading from the
> library. Do I need other arrangement to assess to the library?
> Please help:
>
>   source("http://www.bioconductor.org/biocLite.R")
>      biocLite("BSgenome")
>      require(BSgenome)
>
>>   available.genomes()

Hi Ram --

Individual genomes need to be installed. See

   installed.genomes()

and

   source("http://bioconductor.org/biocLite.R")
   biocLite("BSgenome.Athaliana.TAIR.TAIR9")

Martin
>
> BioC_mirror = http://bioconductor.org
> Change using chooseBioCmirror().
>   [1] "BSgenome.Amellifera.BeeBase.assembly4"
>   [2] "BSgenome.Amellifera.UCSC.apiMel2"
>   [3] "BSgenome.Athaliana.TAIR.01222004"
>   [4] "BSgenome.Athaliana.TAIR.04232008"
>   [5] "BSgenome.Athaliana.TAIR.TAIR9"
>   [6] "BSgenome.Btaurus.UCSC.bosTau3"
>   [7] "BSgenome.Btaurus.UCSC.bosTau4"
>   [8] "BSgenome.Celegans.UCSC.ce2"
>   [9] "BSgenome.Celegans.UCSC.ce6"
> [10] "BSgenome.Cfamiliaris.UCSC.canFam2"
> [11] "BSgenome.Dmelanogaster.UCSC.dm2"
> [12] "BSgenome.Dmelanogaster.UCSC.dm3"
> [13] "BSgenome.Drerio.UCSC.danRer5"
> [14] "BSgenome.Drerio.UCSC.danRer6"
> [15] "BSgenome.Ecoli.NCBI.20080805"
> [16] "BSgenome.Ggallus.UCSC.galGal3"
> [17] "BSgenome.Hsapiens.UCSC.hg17"
> [18] "BSgenome.Hsapiens.UCSC.hg18"
> [19] "BSgenome.Hsapiens.UCSC.hg19"
> [20] "BSgenome.Mmusculus.UCSC.mm8"
> [21] "BSgenome.Mmusculus.UCSC.mm9"
> [22] "BSgenome.Ptroglodytes.UCSC.panTro2"
> [23] "BSgenome.Rnorvegicus.UCSC.rn4"
> [24] "BSgenome.Scerevisiae.UCSC.sacCer1"
> [25] "BSgenome.Scerevisiae.UCSC.sacCer2"
>
>> library(BSgenome.Athaliana.TAIR.TAIR9)
> Error in library(BSgenome.Athaliana.TAIR.TAIR9) :
>    there is no package called 'BSgenome.Athaliana.TAIR.TAIR9'
>
>> library("BSgenome.Athaliana.TAIR.TAIR9")
> Error in library("BSgenome.Athaliana.TAIR.TAIR9") :
>    there is no package called 'BSgenome.Athaliana.TAIR.TAIR9'
>>   library("BSgenome.Hsapiens.UCSC.hg17")
> Error in library("BSgenome.Hsapiens.UCSC.hg17") :
>    there is no package called 'BSgenome.Hsapiens.UCSC.hg17'
>
> Am I missing some dependencies? Please help:
>
>   --
>
> Ram H
>
> 	[[alternative HTML version deleted]]
>
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