flowFPPlex: Fingerprint collection constructor.
In holyst/flowFP: Fingerprinting for Flow Cytometry

Description Usage Arguments Details Value Author(s) See Also Examples

This constructor creates a flowFPPlex, which is a collection of flowFPs.

1	flowFPPlex(fingerprints = NULL)

fingerprints

List of flowFPs, or NULL. If NULL an empty flowFPPlex will be prepared, to which flowFPs may be added with append-methods.

A flowFPPlex is a container object for a collection of flowFPs. It is useful in several ways. First, multiple-tube panels are often used to assay more reagents than can be done on a particular instrument. Second, it is sometimes useful to represent the same data with multiple flowFPModels.

Suppose that we have collected data from 1,000 patients, using an 8-tube panel. Imagine that Tubes 1 and 8 are isotype and viability tubes, respectively (we will ignore these tubes for now). The remaining Tubes 2-7 are of interest from a fingerprinting perspective. We wish to treat them as a unit. We might then create models that represent parameters in each of the tubes, across some (or all) of the patient samples (say, mod2, mod3, ..., mod7). We could then create corresponding flowFPs (say, fp2, fp3, ..., fp7). These can now be combined and treated as a single object of type flowFPPlex, as:

> plex <- flowFPPlex(c(fp2, fp3, fp4, fp5, fp6, fp7))

or if you prefer,

> plex <- flowFPPlex (fingerprints=NULL)
> plex <- append(plex, c(fp2, fp3, fp4, fp5, fp6, fp7))

The counts or density matrices can then be extracted simply using methods provided in flowFPPlex-class.

The second idea is to use multiple models to represent the same data. In this case we might create a model from, say, the "Normal" instances (call it mod\_norm), and another model from the "Cancer" instances (mod\_cancer). We might wish to do this to enhance the detection of regions of the distribution that are characteristically dominated by one type or the other. If our flowSet of all instances is called "fs1", then our two representations would be:

> fp_norm <- flowFP (fs1, mod_norm)
> fp_cancer <- flowFP (fs2, mod_cancer)

and the plex is

plex <- flowFPPlex (c(fp_norm, fp_cancer))

Returns a flowFPPlex.

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

flowFPPlex-class, flowFP

data(fs1)
data(fs2)
mod1 <- flowFPModel (fs1, parameters=c(2,5))
mod2 <- flowFPModel (fs2, parameters=c(2,5))
fp1_1 <- flowFP (fs1, mod1)
fp1_2 <- flowFP (fs1, mod2)

plex <- flowFPPlex(c(fp1_1, fp1_2))