percent.classified: Calculate Percent of OTUs Classified at a Given Taxonomic...

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function consumes an OTU table, and a vector containing taxnomic ranks, then returns what percent of OTUs in the given table are classified at each taxonomic rank.

Usage

percent.classified(data, ranks=c("f","g"))

Arguments

data	a list of OTU tables to be processed. See also RAM.input.formatting
ranks	a vector containing the taxonomic ranks you are interested in (see ?RAM.rank.formatting for formatting details).

Value

A list of numeric vectors, containing the result for each taxonomic rank.

Author(s)

Wen Chen and Joshua Simpson.

Examples

data(ITS1, ITS2)
data <- list(ITS1=ITS1, ITS2=ITS2)
# find what percent of OTUs classified at family and genus 
# levels 
percent.classified(data=data, ranks=c("f","g"))

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-3
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
$ITS1
$ITS1$`%_OTU_classified_at_family_level:`
[1] 57.9932

$ITS1$`%_OTU_classified_at_genus_level:`
[1] 49.89371


$ITS2
$ITS2$`%_OTU_classified_at_family_level:`
[1] 62.72016

$ITS2$`%_OTU_classified_at_genus_level:`
[1] 42.73973

RAM documentation built on May 2, 2019, 3:04 p.m.