assignmentData: assignmentData

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

Description

These accessors access and replace the assignmentData slot of OTUbase objects. assignmentData is an AnnotatedDataFrame. assignmentData and assignmentData<- access and replace this AnnotatedDataFrame. assignmentLabels and assignmentLabels<- access and replace the labels of this AnnotatedDataFrame. aData and aData<- access and replace the dataframe component of the AnnotatedDataFrame.

assignmentNames returns the assignment names present in the assignmentData slot.

Usage

    aData(object,...)
    aData(object)<-value
    assignmentData(object,...)
    assignmentData(object)<-value
    assignmentLabels(object,...)
    assignmentLabels(object)<-value
    assignmentNames(object,...)

Arguments

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

Value

aData returns a dataframe. assignmentData returns an AnnotatedDataFrame. assignmentLabels returns a character. assignmentNames returns a character.

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 aData dataframe
aData(soginOTU)

## get the assignmentData slot
assignmentData(soginOTU)

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