lintGml2-class: Class lintGml2

In flowCore: flowCore: Basic structures for flow cytometry data

Description

Linear transformation as parameterized in Gating-ML 2.0.

Details

lintGml2 is defined by the following function:

bound(f, boundMin, boundMax) = max(min(f,boundMax),boundMin))

where

f(parameter, T, A) = (parameter + A) / (T + A)

This transformation provides a linear display that maps scale values from the [-A, T] interval to the [0, 1] interval. However, it is defined for all x in R including outside of the [-A, T] interval.

In addition, if a boundary is defined by the boundMin and/or boundMax parameters, then the result of this transformation is restricted to the [boundMin,boundMax] interval. Specifically, should the result of the f function be less than boundMin, then let the result of this transformation be boundMin. Analogically, should the result of the f function be more than boundMax, then let the result of this transformation be boundMax. The boundMin parameter shall not be greater than the boundMax parameter.

Slots

.Data

Object of class function.

T

Object of class numeric – positive constant (top of scale value).

A

Object of class numeric – non-negative constant that is less than or equal to T; it is determining the bottom end of the transformation.

parameters

Object of class "transformation" – flow parameter to be transformed.

transformationId

Object of class "character" – unique ID to reference the transformation.

boundMin

Object of class numeric – lower bound of the transformation, default -Inf.

boundMax

Object of class numeric – upper bound of the transformation, default Inf.

Objects from the Class

Objects can be created by calls to the constructor

lintGml2(parameter, T, A, transformationId, boundMin, boundMax)

Extends

Class singleParameterTransform, directly.

Class transform, by class singleParameterTransform, distance 2.

Class transformation, by class singleParameterTransform, distance 3.

Class characterOrTransformation, by class singleParameterTransform, distance 4.

Note

The linear transformation object can be evaluated using the eval method by passing the data frame as an argument. The transformed parameters are returned as a matrix with a single column. (See example below)

Author(s)

Spidlen, J.

References

Gating-ML 2.0: International Society for Advancement of Cytometry (ISAC) standard for representing gating descriptions in flow cytometry. http://flowcyt.sourceforge.net/gating/20141009.pdf

See Also

linearTransform, transform-class, transform

Other mathematical transform classes: EHtrans-class, asinht-class, asinhtGml2-class, dg1polynomial-class, exponential-class, hyperlog-class, hyperlogtGml2-class, invsplitscale-class, logarithm-class, logicletGml2-class, logtGml2-class, quadratic-class, ratio-class, ratiotGml2-class, sinht-class, splitscale-class, squareroot-class, unitytransform-class

Examples

myDataIn <- read.FCS(system.file("extdata", "0877408774.B08", 
    package="flowCore"))
myLinTr1 <- lintGml2(parameters = "FSC-H", T = 1000, A = 0, 
    transformationId="myLinTr1")
transOut <- eval(myLinTr1)(exprs(myDataIn))

flowCore documentation built on Nov. 8, 2020, 5:19 p.m.