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

Description

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

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

Objects from the Class

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

Slots

.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

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.

Methods

No methods defined with class "hyperlog" in the signature.

Note

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)

Author(s)

Gopalakrishnan N, F.Hahne

References

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

 1 2 3 4  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))