splitscale-class: Class "splitscale"

In flowCore: flowCore: Basic structures for flow cytometry data

Description

The split scale transformation class defines a transformation that has a logarithmic scale at high values and a linear scale at low values. The transition points are chosen so that the slope of the transformation is continuous at the transition points.

Details

The split scale transformation is defined by the function

f(parameter,r,maxValue,transitionChannel) = a*parameter+ b, parameter<=t

(parameter,r,maxValue,transitionChannel) = log_{10}(c*parameter)*\frac{r}{d}, parameter > t

where,

b=\frac{transitionChannel}{2}

d=\frac{2*log_{10}(e)*r}{transitionChannel} + log_{10}(maxValue)

t=10^{log_{10}t}

a= \frac{transitionChannel}{2*t}

log_{10}ct=\frac{(a*t+b)*d}{r}

c=10^{log_{10}ct}

Slots

.Data

Object of class "function".

r

Object of class "numeric" – a positive value indicating the range of the logarithmic part of the display.

maxValue

Object of class "numeric" – a positive value indicating the maximum value the transformation is applied to.

transitionChannel

Object of class "numeric" – non negative value that indicates where to split the linear vs. logarithmic transformation.

parameters

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

transformationId

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

Objects from the Class

Objects can be created by calls to the constructor splitscale(parameters,r,maxValue,transitionChannel,transformationId)

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 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

See Also

invsplitscale

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, ratiotGml2-class, sinht-class, squareroot-class, unitytransform-class

Examples

  dat <- read.FCS(system.file("extdata","0877408774.B08",package="flowCore"))
  sp1<-splitscale("FSC-H",r=768,maxValue=10000,transitionChannel=256)
  transOut<-eval(sp1)(exprs(dat))

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