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Last data update: 2014.03.03

R: immunoClust EMt-iteration on Cell-events given initial Model...

cell.FitModel

R Documentation

immunoClust EMt-iteration on Cell-events given initial Model Parameters

Description

The function fits initial model parameters to specific observed cell event data. The function returns the cluster information of the fitted model in an object of class immunoClust.

Usage

cell.FitModel(x, data, B=50, tol=1e-5, bias=0.5, modelName="mvt" )

cell.Classify(x, data, modelName="mvt" )

Arguments

`x`	An immunoClust object with the initial model parameter (parameters, K, w, mu, sigma).
`data`	A numeric matrix, data frame of observations, or object of class flowFrame.
`B`	The maximum number of EMt-iterations.
`tol`	The tolerance used to assess the convergence of the EMt-algorithms.
`bias`	The ICL-bias used in the EMt-algorithm.
`modelName`	Used mixture model; either `"mvt"` or `"mvn"` for a t- or Gaussian mixture model respectively.

Details

These functions are wrapper of the functions cell.EM and cell.Estimation, when model cluster parameters are combined in an object of class immunoClust and are used in the iterative cell event clustering process cell.process of immunoClust and are not intended to be called directly.

Value

The fitted model cluster information in an object of class immunoClust.

Author(s)

Till SÃ¶rensen till-antoni.soerensen@charite.de

References

SÃ¶rensen, T., Baumgart, S., Durek, P., GrÃ¼tzkau, A. and HÃ¤upl, T. immunoClust - an automated analysis pipeline for the identification of immunophenotypic signatures in high-dimensional cytometric datasets. Cytometry A (accepted).

Examples

data(dat.fcs)
data(dat.exp)
r1 <- dat.exp[[1]]
dat.trans <- trans.ApplyToData(r1, dat.fcs)
r2 <- cell.FitModel(r1, dat.trans)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(immunoClust)
Loading required package: grid
Loading required package: lattice
Loading required package: flowCore
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/immunoClust/cell.FitModel.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cell.FitModel
> ### Title: immunoClust EMt-iteration on Cell-events given initial Model
> ###   Parameters
> ### Aliases: cell.FitModel cell.Classify
> 
> ### ** Examples
> 
> data(dat.fcs)
> data(dat.exp)
> r1 <- dat.exp[[1]]
> dat.trans <- trans.ApplyToData(r1, dat.fcs)
> r2 <- cell.FitModel(r1, dat.trans)
EM takes 0.033 mins minutes

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>