subOTUset: subOTUset

In OTUbase: Provides structure and functions for the analysis of OTU data

Description

Function to get a subset of an OTUset object.

Usage

subOTUset(object, samples, otus)

Arguments

object	An OTUset object
samples	A list of sample names
otus	A list of OTU names

Value

subOTUset returns an OTUset

Examples

## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get subset of soginOTU

subOTUset(soginOTU, samples=getSamples(soginOTU, colnum="Site", value="Labrador", exact=FALSE))

OTUbase documentation built on Nov. 8, 2020, 8:24 p.m.