Check if a species is supported and available

Given a species name, it checkes whether is supported, and if supported, check whether the annotation package is installed.

artmsIsSpeciesSupported(species, verbose = TRUE)

Arguments

species

(char) The species name. Species currently supported as part of artMS: HUMAN MOUSE And the following species can be used as well, but the user needs to install the corresponding org.db package: ANOPHELES (install.packages(org.Ag.eg.db)) BOVINE (install.packages(org.Bt.eg.db)) WORM (install.packages(org.Ce.eg.db)) CANINE (install.packages(org.Cf.eg.db)) FLY (install.packages(org.Dm.eg.db)) ZEBRAFISH (install.packages(org.Dr.eg.db)) CHICKEN (install.packages(org.Gg.eg.db)) RHESUS (install.packages(org.Mmu.eg.db)) CHIMP (install.packages(org.Pt.eg.db)) RAT (install.packages(org.Rn.eg.db)) YEAST (install.packages(org.Sc.sgd.db)) PIG (install.packages(org.Ss.eg.db)) XENOPUS (install.packages(org.Xl.eg.db))

verbose

(logical) TRUE (default) shows function messages

Value

(string) Name of the package for the given species

Examples

# Should return TRUE
artmsIsSpeciesSupported(species = "HUMAN")
#> [1] "org.Hs.eg.db"
artmsIsSpeciesSupported(species = "CHIMP")
#> ---(-) The package <org.Pt.eg.db> is not installed in your system.
#>            Just run: install.packages('org.Pt.eg.db') and try again
#> [1] FALSE