abundance: abundance

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

Description

abundance generates an abundance table. This table can be either weighted or unweighted.

Usage

abundance(object, ...)

Arguments

object	An OTUset or a TAXset object
...	Additional arguments. These will depend on if the object is an OTUset or a TAXset object.

Details

These are other arguments passed to abundance

• taxCol If generating the abundance from a TAXset object, taxCol selects the column of the tax dataframe from which to calculate the abundance.

• assignmentCol If generating the abundance from an OTUset object assignmentCol will select a column of the assignmentData dataframe to use when calculating abundance. This will override the default of creating an abundance table of the OTUs and instead create an abundance table of a column in the assignmentData dataframe.

• sampleCol sampleCol generates the abundance table using a column in the sampleData data fram instead of the default of using the sampleID.

• collab An optional parameter that selets a column of the sampleData dataframe to use when labeling the columns of the abundance table.

• weighted By default this is FALSE. When set to TRUE abundance will return proportional abundances.

Value

The returned value will be 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")

## calculate abundance
abundance(soginOTU, collab="Site")

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