tableSpecies: Construct a Genus-Species Data Frame

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

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)

Example output

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