artmsIsSpeciesSupported: Check if a species is supported and available

View source: R/annotations.R

artmsIsSpeciesSupportedR Documentation

Check if a species is supported and available

Description

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

Usage

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")
artmsIsSpeciesSupported(species = "CHIMP")

biodavidjm/artMS documentation built on July 7, 2023, 12:24 p.m.