OTUbase (version 1.22.0)

readOTUset: readOTUset

Description

This function reads in data and creates an OTUset object

Usage

readOTUset(dirPath, otufile, level, fastafile, qualfile, samplefile, sampleADF, assignmentADF, sADF.names, aADF.names, rdp=F, otufiletype)

Arguments

dirPath

The directory path were the datafile are located. This is the current directory by default.

otufile

The OTU file. The only format currently supported is the Mothur format for .list files.

level

The OTU clustering level. By default this is 0.03. This level must correspond to levels present in the otufile.

fastafile

The fasta file. This is read in by ShortRead.

qualfile

The quality file. This is read in by ShortRead.

samplefile

The sample file. Currently this must be in Mothur format (.groups).

sampleADF

The sample meta data file. This is in AnnotatedDataFrame format.

assignmentADF

The assignment meta data file (the OTU meta data). This is generally in AnnotatedDataFrame format although it is also possible to read in an RDP classification file if there is only one read classification for each cluster and rdp=TRUE.

sADF.names

The column of the sampleADF file that has the sample names.

aADF.names

The column of the assignmentADF file that has the assignment names.

rdp

By default this is FALSE. Change to TRUE if assignmentADF is an RDP classification file. The RDP file must be in the fixed format.

otufiletype

The type of OTU file. Takes values "mothur", "cdhit", and "blastclust". Defaults to "mothur".

Examples

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")

soginOTU