.OTUset-class: "OTUset" class for OTU data

Description

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.

Arguments

Slots

OTUsetB includes Slots id, sampleID, otuID, sampleData, assignmentData. OTUsetF includes Slots id sampleID, otuID, sampleData, assignmentData, sread. OTUsetQ includes Slots id sampleID, otuID, sampleData, assignmentData, sread, quality.

Methods

Methods include:

id: provides access to the id slot of object
sampleID: provides access to the sampleID slot of object
otuID: provides access the otuID slot of object
sampleData: provides accesss the sampleData slot of object
assignmentData: provides access the assignmentData slot of object
sread: provides access to the sread slot of object
quality: provides access to the quality slot of object
seqnames: returns the first word of the id line. Intended to extract the sequence name from other sequence information.
nsamples: returns the number of samples in an OTUset object
notus: returns the number of OTUs in an OTUset object
show: signature(object=".OTUset"): provides a brief summary of the object, including its class, number of sequences, number of samples, and number of OTUs.

Examples

Run this code

showClass(".OTUset")
showMethods(class=".OTUset")
showClass("OTUsetQ")

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