This class provides a way to store and manipulate operational taxonomic unit data. ".OTUset" is inherited by "OTUsetQ", "OTUsetF", and "OTUsetB". The user will want to use "OTUsetQ" when quality data is available, "OTUsetF" when sequence data (without quality data) is available, and "OTUsetB" when only OTU and sample data are available.
This class provides a way to store and manipulate read-classification data. ".TAXset" is inherited by "TAXsetQ", "TAXsetF", and "TAXsetB". The user will want to use "TAXsetQ" when quality data is available, "TAXsetF" when sequence data (without quality data) is available, and "TAXsetB" when only classification and sample data are available.
accessors
(Package: OTUbase) :
Accessor functions for OTUset and TAXset objects
These functions provide access to some of the slots of OTUset and TAXset objects. otuID returns the otuID slot of OTUset objects. sampleID returns the sampleID slot of both OTUset and TAXset objects. tax and tax<- return and replace the tax slot of TAXset objects.
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.
This function is a wrapper for the vegan function vegedist and hclust. It allows the user to cluster samples using a number of different distance measure and clustering methods. Please see the documentation for vegedist and hclust for a more indepth explanation.
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).
Various functions. notus returns the number of OTUs in an OTUset object. nsamples returns the number of samples in either an OTUset or a TAXset object. seqnames returns the sequence names of the OTUset or TAXset object without the extra information commonly present with the id.
providing 
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