eudysbiome (version 1.2.0)

microAnnotate: Genus Annotation

Description

Annotates given genera as harmful or harmless based on either our manually curated, harmful Genus-Species table in data harmGenera of this package or user defined table.

Usage

microAnnotate(microbe, species = TRUE, annotated.micro = NULL)

Arguments

microbe

a genus list to be annotated; a Genus-Species data frame which represents the genera and the included corresponding species is recommended to be provided by users for the more accurate annotations, see tableSpecies.

species

logical, specifying if the species are provided in the microbe for the annotations; default to TRUE.

annotated.micro

the annotated genera which are used for the annotation of microbe, it could either be loaded from the data harmGenera or defined by users.

Value

The annotated genera.

Examples

#load the genera to be annotated
library(eudysbiome)
data(diffGenera)

#load the curated Genus-Species annotation table
data(harmGenera)

microAnnotate(microbe = diffGenera, species = TRUE,
           annotated.micro = harmGenera)