[BioC] Biobase use problem

[Sean Davis]

On Sat, Sep 17, 2011 at 4:38 PM, Ram H. Sharma <sharma.ram.h at gmail.com> 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()
>
> 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:

Hi, Ram.

You need to install the package first:

biocLite('BSgenome.Athaliana.TAIR.TAIR9')

Then:

library('BSgenome.Athaliana.TAIR.TAIR9')

Sean