OTUbase (version 1.22.0)

otherGenerics: Other Generics

Description

Various functions. notus returns the number of OTUs in an OTUset object. nsamples returns the number of samples in either an OTUset or a TAXset object. seqnames returns the sequence names of the OTUset or TAXset object without the extra information commonly present with the id.

Usage

notus(object, ...) nsamples(object, ...) seqnames(object, ...)

Arguments

object

An OTUset or a TAXset object.

...

Other arguments. These are currently nonfunctional.

Examples

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 the number of OTUs
notus(soginOTU)

## get the number of samples
nsamples(soginOTU)