flowFP-class: Fingerprint class description.

Description

This class represents fingerprints generated from a model derived from a flowFrame or flowSet.

Arguments

Objects from the Class

Objects are created by calling the constructor flowFP.

Slots

counts:: This matrix is organized such that rows correspond to individual flowFrames, and columns to the bins in the underlying flowFPModel. A matrix element thus represents the number of events in a single bin from a single flowFrame. The sum of each row will equal the total number of events in the corresponding flowFrame.
tags:: This list specifies the bin number to which each event is assigned. There is a list element for each instance in the object. Each list element is a integer vector whose length is the number of events in the corresponding flowFrame.
sampleNames:: Names of instances, taken from the flowSet on construction.
sampleClasses:: Factor object describing the category of each instance. (e.g. "Normal" or "Diseased")
name:: Inherited from flowFPModel.
parameters:: Inherited from flowFPModel.
nRecursions:: Inherited from flowFPModel.
trainingSet:: Inherited from flowFPModel.
trainingSetParams:: Inherited from flowFPModel.
dequantize:: Inherited from flowFPModel.
split_val:: Inherited from flowFPModel.
split_axis:: Inherited from flowFPModel.
binBoundary:: Inherited from flowFPModel.
.cRecursions:: Inherited from flowFPModel.
.tmp_tags:: Inherited from flowFPModel.

Extends

Class flowFPModel, directly.

Methods

[: Used to select a subset of a fingerprint object.
counts: Returns the counts matrix of a fingerprint object. See counts.
length: Returns the number of instances in the fingerprint object.
nbins: Returns the number of bins (equal to 2^nRecursions) in the fingerprint object.
sampleClasses: Returns the sampleClasses slot of the fingerprint object.
sampleClasses<-: Set method for the sampleClasses slot of the fingerprint object. Note that the length of the provided object must be equal to the number of instances in the fingerprint object. If the provided object is not a factor it will be coerced to one.
tags: Returns the tags slot. See tags.
show: Shows the contents of the fingerprint object.
summary: Gives a summary of the fingerprint object.

References

M. Roederer, et. al. (2001) Probability Binning Comparison: A Metric for Quantitating Multivariate Distribution Differences, Cytometry 45, 47-55.

W. Rogers et. al. (2008) Cytometric Fingerprinting: Quantitative Characterization of Multivariate Distributions, Cytometry Part A 73, 430-441.

Examples

Run this code


	# load a flowSet to use as an example.
	library(flowFP)
	data(fs1)
	model <- flowFPModel(fs1, parameters=c(4,5), nRecursions=6)
	
	fp <- flowFP(fs1, model)
	
	plot(fp)

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