microAnnotate {eudysbiome} | R Documentation

## 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)

[Package eudysbiome version 1.16.0 Index]