other_generics: Other Generics

Description Usage Arguments Examples

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

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

Arguments

object

An OTUset or a TAXset object.

...

Other arguments. These are currently nonfunctional.

Examples

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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)

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