hyperlog-class: Class "hyperlog"
In flowCore: flowCore: Basic structures for flow cytometry data

Description Slots Objects from the Class Extends Note Author(s) References See Also Examples

Hyperlog transformation of a parameter is defined by the function

f(parameter,a,b)=root{EH(y,a,b)-parameter}

where EH is a function defined by

EH(y,a,b) = 10^{(\frac{y}{a})} + \frac{b*y}{a}-1, y>=0

EH(y,a,b)= -10^{(\frac{-y}{a})} + \frac{b*y}{a}+1, y<0

.Data: Object of class "function".
a: Object of class "numeric" – numeric constant treater than zero.
b: Object of class "numeric" numeric constant greater than zero.
parameters: Object of class "transformation" – flow parameter to be transformed.
transformationId: Object of class "character" – unique ID to reference the transformation.

Objects can be created by calls to the constructor hyperlog(parameter,a,b,transformationId)

Class "singleParameterTransform", directly.

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

Class "transformation", by class "singleParameterTransform", distance 3.

Class "characterOrTransformation", by class "singleParameterTransform", distance 4.

The 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)

Gopalakrishnan N, F.Hahne

Gating-ML Candidate Recommendation for Gating Description in Flow Cytometry V 1.5

EHtrans

Other mathematical transform classes: EHtrans-class, asinht-class, asinhtGml2-class, dg1polynomial-class, exponential-class, hyperlogtGml2-class, invsplitscale-class, lintGml2-class, logarithm-class, logicletGml2-class, logtGml2-class, quadratic-class, ratio-class, ratiotGml2-class, sinht-class, splitscale-class, squareroot-class, unitytransform-class

  dat <- read.FCS(system.file("extdata","0877408774.B08",
  package="flowCore"))
  hlog1<-hyperlog("FSC-H",a=1,b=1,transformationId="hlog1")
  transOut<-eval(hlog1)(exprs(dat))