OTUset-class: "OTUset" class for OTU data

In OTUbase: Provides structure and functions for the analysis of 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.

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

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

OTUbase documentation built on Nov. 8, 2020, 8:24 p.m.