.TAXset-class: "TAXset" class for TAX data

Description

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.

Arguments

Slots

TAXsetB includes Slots id, sampleID, tax, sampleData, assignmentData. TAXsetF includes Slots id sampleID, tax, sampleData, assignmentData, sread. TAXsetQ includes Slots id sampleID, tax, 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
tax: provides access the tax 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 TAXset object
show: signature(object=".TAXset"): provides a brief summary of the object, including its class, number of sequences, and number of samples.

Examples

Run this code

showClass(".TAXset")
showMethods(class=".TAXset")
showClass("TAXsetQ")

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