ratiotGml2-class: Class "ratiotGml2"

In flowCore: flowCore: Basic structures for flow cytometry data

Description

Ratio transformation as parameterized in Gating-ML 2.0.

Details

ratiotGml2 is defined by the following function:

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

where

f(p1, p2, A, B, C) = A * (p1 - B) / (p2 - C)

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.

numerator

Object of class "transformation" – flow parameter to be used as numerator in the transformation function.

denominator

Object of class "transformation" – flow parameter to be used as denominator in the transformation function.

pA

Object of class numeric constant A.

pB

Object of class numeric constant B.

pC

Object of class numeric constant C.

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

ratiotGml2(p1, p2, A, B, C, transformationId, boundMin, boundMax)

Extends

Class "transform", directly.

Class "transformation", by class "transform", distance 2.

Class "characterOrTransformation", by class "transform", distance 3.

Note

The ratiotGml2 transformation object can be evaluated using the eval method by passing the data frame as an argument. The transformed parameters are returned as matrix with one 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

ratio, transform-class, transform

Other mathematical transform classes: EHtrans-class, asinht-class, asinhtGml2-class, dg1polynomial-class, exponential-class, hyperlog-class, hyperlogtGml2-class, invsplitscale-class, lintGml2-class, logarithm-class, logicletGml2-class, logtGml2-class, quadratic-class, ratio-class, sinht-class, splitscale-class, squareroot-class, unitytransform-class

Examples

myDataIn <- read.FCS(system.file("extdata", "0877408774.B08", 
    package="flowCore"))
myRatioT <- ratiotGml2("FSC-H", "SSC-H", pA = 2, pB = 3, 
    pC = -10, transformationId = "myRatioT")
transOut <- eval(myRatioT)(exprs(myDataIn))

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