logtGml2-class: Class logtGml2

In flowCore: flowCore: Basic structures for flow cytometry data

Description

Log transformation as parameterized in Gating-ML 2.0.

Details

logtGml2 is defined by the following function:

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

where

f(parameter, T, M) = (1/M) * log10(x/T) + 1

This transformation provides a logarithmic display that maps scale values from the (0, T] interval to the (-Inf, 1] interval such that the data value T is mapped to 1 and M decades of data are mapped into the interval. Also, the limit for x going to 0 is -Inf.

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).

M

Object of class numeric – positive constant (number of decades).

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

logtGml2(parameter, T, M, 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 log 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

logTransform, 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, 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"))
myLogTr1 <- logtGml2(parameters = "FSC-H", T = 1023, M = 4.5, 
    transformationId="myLogTr1")
transOut <- eval(myLogTr1)(exprs(myDataIn))

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