flowFit (version 1.10.0)

parentFitting: Fitting a parent population

Description

Estimate the proliferation of a cell population in cell-tracking dye studies. parentFitting: fit the parent population

Usage

parentFitting(flowframe, channel, 
              estimatedPeakPosition = NA, 
              estimatedPeakSize = NA, 
              dataRange = NA,  
              logDecades = NA, 
              binning = TRUE, 
              breaks = 1024, 
              dataSmooth = TRUE, 
              smoothWindow = 2, 
              fixedModel = FALSE, 
              fixedPars = NA, 
              verbose = FALSE )

Arguments

flowframe

An object of class flowFrame from flowCore

channel

FACS column/channel (flowFrame column)

estimatedPeakPosition

Estimated peak position. If not provided will be used the exprs mean

estimatedPeakSize

Estimated peak size. If not provided will be used the exprs standard deviation

dataRange

Number of digital data points on the machine. If not provided will be extracted from flowFrame using keyword

logDecades

FACS dynamic range (log decades). If not provided will be extracted from flowFrame using keyword

binning

Should I bin data? Some FACS have a large data range (Es: FACSCanto have 65536 data points, may be is convenient in this case to group data in bins to avoid acquiring too many cells). If you have you data log tranformed in range 0-5 it is mandatory to bin data

breaks

How many breaks if I bin data?

dataSmooth

Should I smooth data with a Kolmogorov-Zurbenko low-pass linear filter?

smoothWindow

Window used to smooth data with the Kolmogorov-Zurbenko low-pass linear filter.

fixedModel

Should I use a model with fixed parameters? (Peak Position or Size).

fixedPars

A list of fixed parameters. If you give me a value, I use that value, otherwise I use estimates (check examples)

verbose

Verbose mode.

Value

• return a parentFittingData object

Details

The formula used to fit the parent population:

$$a^2\exp\frac{(x - \mu)^2}{2\sigma^2}$$

The algorithm estimate the position ($\mu$) and size ($\sigma$) of the Parent Population.

References

1. Timur V. Elzhov, Katharine M. Mullen and Ben Bolker (2012).minpack.lm: R interface to the Levenberg-Marquardt nonlinear least-squares algorithm found in MINPACK.

See Also

proliferationFitting

Examples

if(require(flowFitExampleData)){
    # CFSE
    data(QuahAndParish)
    parent.fitting.cfse <- parentFitting(QuahAndParish[[1]], "<FITC-A>")

    parent.fitting.cfse
    summary(parent.fitting.cfse)
    confint(parent.fitting.cfse)
    coef(parent.fitting.cfse)
    plot(parent.fitting.cfse)
    Data(parent.fitting.cfse)

    # PKH26
    data(PKH26data)
    parent.fitting <-  parentFitting(PKH26data[[1]], "FL2-Height LOG")
    parent.fitting
    summary(parent.fitting)
    confint(parent.fitting)
    coef(parent.fitting)
    plot(parent.fitting)
    Data(parent.fitting)

    # fixedModel with estimates
    parent.fitting <-  parentFitting(PKH26data[[1]], "FL2-Height LOG", 
                                     fixedModel=TRUE, fixedPars=list(M=NA,S=NA))

    # fixedModel with user values
    parent.fitting <-  parentFitting(PKH26data[[1]], "FL2-Height LOG", 
                                     fixedModel=TRUE, fixedPars=list(M=810,S=16))

    # fixedModel with locked Peak Size (one fixed parameter)
    parent.fitting <-  parentFitting(PKH26data[[1]], "FL2-Height LOG", 
                                     fixedModel=TRUE, fixedPars=list(S=17))
  }