R: Accessor functions for OTUset and TAXset objects

accessors {OTUbase}

R Documentation

Accessor functions for OTUset and TAXset objects

Description

These functions provide access to some of the slots of OTUset and TAXset objects. otuID returns the otuID slot of OTUset objects. sampleID returns the sampleID slot of both OTUset and TAXset objects. tax and tax<- return and replace the tax slot of TAXset objects.

Usage

    sampleID(object, ...)
    otuID(object, ...)
    tax(object, ...)
    tax(object)<-value

Arguments

`object`	An OTUset or a TAXset object
`value`	The replacement value for `tax`
`...`	Added for completeness. Enables the passing of arguments.

Value

sampleID and otuID return a character. tax returns a data.frame.

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 the sampleID slot
sampleID(soginOTU) 

## get the otuID slot
otuID(soginOTU)