subTAXset: subTAXset

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

Description

Function to get a subset of an TAXset object.

Usage

subTAXset(object, samples)

Arguments

object	An TAXset object
samples	A list of sample names

Value

subTAXset returns an TAXset

Examples

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

## read in data into TAXset object
soginTAX <- readTAXset(dirPath=dirPath, samplefile="sogin.groups", fastafile="sogin.fasta", taxfile="sogin.unique.fix.tax",namefile="sogin.names", sampleADF="sample_metadata.txt")

## get subset of soginTAX

subTAXset(soginTAX, samples=getSamples(soginTAX, colnum="Site", value="Labrador", exact=FALSE))

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