OTUbase (version 1.22.0)

other_functions: Other functions

Description

These are other functions available. Caution is advised when using them. Some are still in development and others only work on specific objects (OTUset or TAXset).

Usage

getOTUs(object, colnum, value, exact) getSamples(object, colnum, value, exact) o_diversity(object, ...) o_estimateR(object, ...)

Arguments

object

An OTUset or a TAXset object.

colnum

The column of the sampleData or assignmentData dataframe that contains the value.

value

The desired value.

exact

If exact=T value must match perfectly. If exact=F value will grep instead of match.

...

Other arguments. Often these are passed to abundance

Details

• getOTUs Returns OTU names that match given values in the assignmentData dataframe.

• getSamples Returns sample names that match given values in the sampleData dataframe.

• o_diversity Wrapper for vegan's diversity function.

• o_estimateR Wrapper for vegan's estimateR function.

• otuseqplot Plots the samples acording to number of OTUs and number of sequences.

• otusize Returns the size of each OTU.

• otuspersample Lists the number of OTUs in each sample.

• rseqplot Plots the samples by estimated richness and number of sequences.

• seqspersample Returns the number of sequences in each sample.

• sharedotus Returns the number of OTUs shared between samples.

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")

getSamples(soginOTU, colnum="Site", value="Labrador", exact=FALSE)

o_estimateR(soginOTU)