proliferationFittingData-class: Class "proliferationFittingData"

In flowFit: Estimate proliferation in cell-tracking dye studies

Description

Provides S4 data structure and basic infrastructure and functions to store proliferation tracking data of the Parent Population.

Objects from the Class

Objects can be created by calls of the form new("proliferationFittingData", flowframe, channel, ...). This class is for internal use.

Slots

data:

Object of class "flowFrame" ~~

channel:

Object of class "character" ~~

estimatedPeakPosition:

Object of class "numeric" ~~

estimatedPeakSize:

Object of class "numeric" ~~

dataRange:

Object of class "numeric" ~~

logDecades:

Object of class "numeric" ~~

estimatedDistance:

Object of class "numeric" ~~

parentPeakPosition:

Object of class "numeric" ~~

parentPeakSize:

Object of class "numeric" ~~

fittingDeviance:

Object of class "numeric" ~~

fixedModel:

Object of class "logical" ~~

fixedPars:

Object of class "list" ~~

generationsDistance:

Object of class "numeric" ~~

heights:

Object of class "list" ~~

generations:

Object of class "numeric" ~~

binning:

Object of class "logical" ~~

breaks:

Object of class "numeric" ~~

dataSmooth:

Object of class "logical" ~~

smoothWindow:

Object of class "numeric" ~~

parStart:

Object of class "list" ~~

dataMatrix:

Object of class "matrix" ~~

dataPoints:

Object of class "data.frame" ~~

modelPoints:

Object of class "data.frame" ~~

model:

Object of class "function" ~~

residFun:

Object of class "function" ~~

lmOutput:

Object of class "nls.lm" ~~

numberOfPeaks:

Object of class "numeric" ~~

Methods

plot

Basic plots for proliferationFittingData objects. Usage: plot(proliferationFittingData, main="Original data and Parent fitting", xlab="FACS data range", ylab="# of Events", showLegend=TRUE, logScale = TRUE, drawGrid = TRUE, ...)

show

Display details about the proliferationFittingData object.

summary

Return a descriptive summary about the proliferationFittingData object.

Data

Return the flowFrame object.

coef

Return coefficients of the model.

confint

Return confidence intervals of the model.

Author(s)

Davide Rambaldi

See Also

proliferationFitting

Examples

  showClass("proliferationFittingData")
  if(require(flowFitExampleData)){
    data(PKH26data)
    parent.fitting <-  parentFitting(PKH26data[[1]], "FL2-Height LOG")
    my.fit <- proliferationFitting(PKH26data[[2]], 
                                   "FL2-Height LOG", 
                                   parent.fitting@parentPeakPosition, 
                                   parent.fitting@parentPeakSize)
    my.fit
    summary(my.fit)
    confint(my.fit)
    coef(my.fit)
    plot(my.fit)
    Data(my.fit)
  }

flowFit documentation built on April 28, 2020, 9:04 p.m.