RAM (version 1.2.1.3)

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

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.

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"))