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.
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 flowFPs 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 flowFPs
to be joined in a plex contain different sampleNames and/or sampleClasses.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 |
flowFPPlex is the constructor for this class. flowFPPlex(fingerprints=NULL)
fingerprints |
Either an single flowFP or a list of flowFPs |
(e.g. fingerprints = c(fp1, fp2)). All of the fingerprints |
| 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 |
W. Rogers et. al. (2008) Cytometric Fingerprinting: Quantitative Characterization of Multivariate Distributions, Cytometry Part A 73, 430-441.
# load a flowSet to use as an example.
library(flowFP)
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