microAnnotate: Genus Annotation

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

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)

Example output

$genera
     Genus micro.anno
1   genus1   harmless
4   genus2   harmless
6   genus3   harmless
7   genus4   harmless
10  genus5   harmless
12  genus6   harmless
16  genus7   harmless
18  genus8   harmless
21  genus9   harmless
26 genus10   harmless

$microbe
     Genus  Species micro.anno
1   genus1 species1   harmless
2   genus1 species2   harmless
3   genus1 species3   harmless
4   genus2 species1   harmless
5   genus2 species2   harmless
6   genus3 species1   harmless
7   genus4 species1   harmless
8   genus4 species2   harmless
9   genus4 species3   harmless
10  genus5 species1   harmless
11  genus5 species2   harmless
12  genus6 species1   harmless
13  genus6 species2   harmless
14  genus6 species3   harmless
15  genus6 species4   harmless
16  genus7 species1   harmless
17  genus7 species2   harmless
18  genus8 species1   harmless
19  genus8 species2   harmless
20  genus8 species3   harmless
21  genus9 species1   harmless
22  genus9 species2   harmless
23  genus9 species3   harmless
24  genus9 species4   harmless
25  genus9 species5   harmless
26 genus10 species1   harmless

eudysbiome documentation built on Nov. 8, 2020, 7:49 p.m.