GenomeInstaller: GenomeInstaller

In brengong/ConservationtextmineR:

Description

Requires a character vector of specified genomes to install and installs them. Installs the following genomes when specified "BSgenome.Hsapiens.UCSC.hg38" "BSgenome.Mmusculus.UCSC.mm9" "BSgenome.Mmusculus.UCSC.mm10" "BSgenome.Rnorvegicus.UCSC.rn6" "BSgenome.Alyrata.JGI.v1" "BSgenome.Amellifera.BeeBase.assembly4" "BSgenome.Athaliana.TAIR.TAIR9" "BSgenome.Btaurus.UCSC.bosTau8" "BSgenome.Celegans.UCSC.ce2" "BSgenome.Celegans.UCSC.ce11" "BSgenome.Cfamiliaris.UCSC.canFam3" "BSgenome.Dmelanogaster.UCSC.dm3" "BSgenome.Drerio.UCSC.danRer10" "BSgenome.Gaculeatus.UCSC.gasAcu1" "BSgenome.Ggallus.UCSC.galGal4" "BSgenome.Mfascicularis.NCBI.5.0" "BSgenome.Mfuro.UCSC.musFur1" "BSgenome.Mmulatta.UCSC.rheMac3" "BSgenome.Osativa.MSU.MSU7" "BSgenome.Ptroglodytes.UCSC.panTro3" "BSgenome.Scerevisiae.UCSC.sacCer3" "BSgenome.Sscrofa.UCSC.susScr3" "BSgenome.Tguttata.UCSC.taeGut2"

Usage

GenomeInstaller(genomes)

Arguments

genomes

A character vector indicating which genomes to install of the following options: "Hsapiens.UCSC.hg38" "Mmusculus.UCSC.mm9" "Mmusculus.UCSC.mm10" "Rnorvegicus.UCSC.rn6" "Alyrata.JGI.v1" "Amellifera.BeeBase.assembly4" "Athaliana.TAIR.TAIR9" "Btaurus.UCSC.bosTau8" "Celegans.UCSC.ce2" "Celegans.UCSC.ce11" "Cfamiliaris.UCSC.canFam3" "Dmelanogaster.UCSC.dm3" "Drerio.UCSC.danRer10" "Gaculeatus.UCSC.gasAcu1" "Ggallus.UCSC.galGal4" "Mfascicularis.NCBI.5.0" "Mfuro.UCSC.musFur1" "Mmulatta.UCSC.rheMac3" "Osativa.MSU.MSU7" "Ptroglodytes.UCSC.panTro3" "Scerevisiae.UCSC.sacCer3" "Sscrofa.UCSC.susScr3" "Tguttata.UCSC.taeGut2"

Value

The specified downloaded genomes

Author(s)

Brendan Gongol

Examples

GenomeInstaller(c("Hsapiens.UCSC.hg38","Mmusculus.UCSC.mm9"))
GenomeInstaller("Apple")

The following code installs all available genomes with this function and attempts to install one genome not available ("APPLE"):
ToInstall <- c("Hsapiens.UCSC.hg38","Mmusculus.UCSC.mm9"
,"Mmusculus.UCSC.mm10","Rnorvegicus.UCSC.rn6"
,"Alyrata.JGI.v1","Amellifera.BeeBase.assembly4"
,"Athaliana.TAIR.TAIR9","Btaurus.UCSC.bosTau8"
,"Celegans.UCSC.ce2","Celegans.UCSC.ce11"
,"Cfamiliaris.UCSC.canFam3","Dmelanogaster.UCSC.dm3"
,"Drerio.UCSC.danRer10","Gaculeatus.UCSC.gasAcu1"
,"Ggallus.UCSC.galGal4","Mfascicularis.NCBI.5.0"
,"Mfuro.UCSC.musFur1","Mmulatta.UCSC.rheMac3"
,"Osativa.MSU.MSU7","Ptroglodytes.UCSC.panTro3"
,"Scerevisiae.UCSC.sacCer3","Sscrofa.UCSC.susScr3"
,"Tguttata.UCSC.taeGut2", "APPLE")
GenomeInstaller(ToInstall)

brengong/ConservationtextmineR documentation built on July 29, 2019, 10:05 a.m.