tableSpecies {eudysbiome} | R Documentation

## Construct a Genus-Species Data Frame

### Description

This function is used to extract only Genus-Species data from the assigned taxonomic paths outputted by `assignTax` and construct a table containing the classified genera and species included in these genera correspondingly.

### Usage

    tableSpecies(tax.file, microbe)

### Arguments

`tax.file` | a taxonomy file with SSU rRNA sequence names and assigned taxonomic paths, see "*.taxonomy" file outputted by `assignTax`.
`microbe` | a character vector specifying the genera used to construct the Genus-Species data frame

### Details

The outputted Genus-Species table can be used as input for the more accurate genus annotation, which annotates genera as `harmful` or `harmless` based on their ability to contribute to mammals' host diseases by `microAnnotate`.

### Value

a Genus-Species data frame, only with the genera specified by `microbe` and the included corresponding species .

### Examples

    #a table with "Lactobacillus" and "Bacteroids" genera and the included species
    genera = c("Lactobacillus","Bacteroides")
    #not excute
    #tableSpecies(tax.file = "test.taxExtract.wang.taxonomy", microbe = genera)

[Package eudysbiome version 1.16.0 Index]