flowFP-package {flowFP} | R Documentation

## Package overview

### Description

This package is used to explore flow cytometry data through the use of fingerprints. The broad aim of the package is to transform flow cytometric data into a form amenable to algorithmic analysis tools. Thus, it is useful to think of flowFP as an intermediate step between the acquisition of high-throughput flow cytometric data and empirical modeling, machine learning and knowledge discovery.

A fingerprint is a feature vector meant to efficiently represent the multivariate probability distribution function for a flow cytometry data set. It is produced by first creating a data-relevant model of a space, and then applying the model to a dataset, thereby producing fingerprints. Model creation is done through the flowFPModel constructor which can be customized via function arguments. After the model is built, it can be applied to arbitrary flowFrames or flowSets using the flowFP constructor. The resulting S4 object implements plotting and summary methods that allow the user to compare and contrast instances, using the `flowFPModel` as a sort of basis representation, akin for example to trigonometric functions in a Fourier Transform.

This package is closely integrated with `flowCore`. You will want to become familiar with it in order to effectively use flowFP.

### Details

Package: | flowFP
Type: | Package
Version: | 1.1.2
Depends: | R(>= 2.5.0), flowCore, flowViz
Collate: | flowFPModel.R flowFP.R
Bioinformatics: | Flowcytometry, CellBasedAssays, Clustering, Statistics, Visualization
License: | Artistic-2.0
Built: | R 2.8.0; unix

### Classes

`flowFPModel-class` is the fundamental class for the flowFP package. It represents the multivariate probability distribution function for a flow cytometry data set. Information is maintained in a number of slots, which should only be accessed through methods, described below, not by direct use of the @ operator. For a complete detailed list of slot names and descriptions look at the `flowFPModel-class` help page.

`flowFP-class` extends the `flowFPModel` and contains additional slots to record the assignment to and number of events in the bins of a `flowFPModel`. Methods are supplied to retrieve and visualize the the contents of a `flowFP`.

`flowFPPlex-class` is a container for a set of congruent `flowFP` objects (by congruent, we mean that each `flowFP` is a description of the same set of instances). When constructing or appending `flowFP`s into a plex, simple error checking is done to ensure each instance in each `flowFP` is equivalent. Both the `sampleNames` and the `sampleClasses` slots are consulted for internal consistency. An error is generated if any of the `flowFP`s to be joined in a plex contain different `sampleNames` and/or s`ampleClasses`.

### Constructors

`flowFPModel` is the constructor for this class.

    flowFPModel(fcs, name="Default Model", parameters=NULL, nRecursions="auto",
                dequantize=TRUE, sampleSize=NULL)

`fcs` | Either an `flowFrame` or a `flowSet` used to create the model.
`name` | Name given the model.
`parameters` | Parameters to consider when constructing the model.(e.g. c(1,5)).
`nRecursions` | The number of level of recursive subdivision.
`dequantize` | Setting this value causes a small incremental value to be added
| to each event starting with 1e-8. This effectively reduces the
| number of duplicate values to break ties when binning.
`sampleSize` | The max number of events to use out of each fcs file in a
| `flowFrame` or `flowSet`.

`flowFP` is the constructor for this class.

    flowFP(fcs, model=NULL, sampleClasses=NULL, ...)

`fcs` | Either an `flowFrame` or a `flowSet` used to create the fingerprint.
`model` | A model created using `flowFPModel` or NULL in which case
| a model will be created from the fcs data supplied.
`sampleClasses` | List of sample class names to be assigned in order to the instances.
`...` | If the `model` is NULL the parameters are passed through to
| `flowFPModel`.

`flowFPPlex` is the constructor for this class.

    flowFPPlex(fingerprints=NULL)

`fingerprints` | Either an single `flowFP` or a list of `flowFP`s
| (e.g. `fingerprints = c(fp1, fp2)`). All of the fingerprints
| must share the same sample names, and class names (or no class names).

### Note

For further information please see the vignette.

### Author(s)

Herb Holyst <holyst@mail.med.upenn.edu>, Wade Rogers <rogersw@mail.med.upenn.edu>

### 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.

### See Also

flowCore, flowViz

### Examples

    	# load a flowSet to use as an example.
    	library(flowFP)

[Package flowFP version 1.40.1 Index]