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

Function to read in data and create a TAXset object

1	readTAXset(dirPath, taxfile, namefile, fastafile, qualfile, samplefile, sampleADF, assignmentADF, sADF.names, aADF.names, type, ...)

`dirPath`	The directory path were the datafile are located. This is the current directory by default.
`taxfile`	The classification file. The default format is RDP's fixed format.
`namefile`	A names file in the Mothur format. This is used to add removed unique sequences back into the dataset.
`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 in AnnotatedDataFrame format.
`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.
`type`	This is the type of taxfile. By default this is the RDP fixed format. However, if `type` is changed to anything else the `read.table` function is used to read in the `taxfile`. In this case the first column of the taxfile must be the sequence names.
`...`	Additional arguments passed to `read.table` to read in the taxfile.

dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into TAXset object
soginTAX <- readTAXset(dirPath=dirPath, samplefile="sogin.groups", fastafile="sogin.fasta", taxfile="sogin.unique.fix.tax", namefile="sogin.names", sampleADF="sample_metadata.txt")

soginTAX