GenomeLoader: GenomeLoader

In brengong/ConservationtextmineR:

Description

Requires a character vector of specified genomes to load and loads them.

Usage

GenomeLoader(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"

Details

Loads the following genomes when specified BSgenome.Mmusculus.UCSC.mm10 BSgenome.Hsapiens.UCSC.hg38 BSgenome.Rnorvegicus.UCSC.rn6 BSgenome.Alyrata.JGI.v1 BSgenome.Amellifera.BeeBase.assembly4 BSgenome.Athaliana.TAIR.TAIR9 BSgenome.Btaurus.UCSC.bosTau8 BSgenome.Celegans.UCSC.ce11 BSgenome.Cfamiliaris.UCSC.canFam3 BSgenome.Dmelanogaster.UCSC.dm6 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

Value

The specified loaded genomes

Author(s)

Brendan Gongol

Examples

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

The following code loads all available genomes with this function and attempts to load one genome not available ("APPLE"):
ToLoad <- 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")
GenomeLoader(ToLoad)

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