microAnnotate: Genus Annotation
In eudysbiome: Cartesian plot and contingency test on 16S Microbial data

Description Usage Arguments Value Examples

View source: R/microAnnotate.R

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.

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

`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.

The annotated genera.

#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)