normalization-class: Class "normalization"
In RGLab/flowCore: flowCore: Basic structures for flow cytometry data

normalization-class

R Documentation

Class "normalization"

Description

Class and methods to normalize a a flowSet using a potentially complex normalization function.

Usage

normalization(parameters, normalizationId="defaultNormalization",
              normFunction, arguments=list())

normalize(data, x,...)

Arguments

`parameters`	Character vector of parameter names.
`normalizationId`	The identifier for the normalization object.
`x`	An object of class `flowSet`.
`normFunction`	The normalization function
`arguments`	The list of additional arguments to `normFunction`
`data`	The `flowSet` to normalize.
`...`	other arguments: see `normalize-methods`for details.

Details

Data normalization of a flowSet is a rather fuzzy concept. The idea is to have a rather general function that takes a flowSet and a list of parameter names as input and applies any kind of normalization to the respective data columns. The output of the function has to be a flowSet again. Although we don't formally check for it, the dimensions of the input and of the output set should remain the same. Additional arguments may be passed to the normalization function via the arguments list. Internally we evaluate the function using do.call and one should check its documentation for details.

Currently, the most prominent example for a normalization function is warping, as provided by the flowStats package.

Value

A normalization object for the constructor.

A flowSet for the normalize methods.

Slots

parameters: Object of class "character". The flow parameters that are supposed to be normalized by the normalization function.
normalizationId: Object of class "character". An identifier for the object.
normFunction: Object of class "function" The normalization function. It has to take two mandatory arguments: x, the flowSet, and parameters, a character of parameter names that are to be normalized by the function. Additional arguments have to be passed in via arguments.
arguments: Object of class "list" A names list of additional arguments. Can be NULL.

Objects from the Class

Objects should be created using the constructor normalization(). See the Usage and Arguments sections for details.

Methods

identifier<-: signature(object = "normalization", value = "character"): Set method for the identifier slot.
identifier: signature(object = "normalization"): Get method for the identifier slot.
normalize: signature(data = "flowSet", x = "normalization"): Apply a normalization to a flowSet.
parameters: signature(object = "normalization"): The more generic constructor.