Probability binning metirc for comparing the probability binned datasets

Description

This function calculates the Probability binning metric proposed by Baggerly et al. The function utilizes the data binned using the proBin and binByRef functions.

Usage

calcPBChiSquare(ctrlRes,sampRes,ctrlCount,sampCount)

Arguments

Value

A list containing the statistic, p.value, observed, expected counts and the residuals

Author(s)

Nishant Gopalakrishnan

See Also

proBin, calcPBChiSquare

Examples

data(GvHD)
# flow frame 1 is treated as  control dataset and used to generate bins
resCtrl<-proBin(GvHD[[1]][,c("FSC-H","SSC-H","Time")],200)  
plotBins(resCtrl,GvHD[[1]],channels=c("FSC-H","SSC-H","Time"),title="Binned control data")
# Same bins are applied to flowFrame 16
resSample<-binByRef(resCtrl,GvHD[[16]][,c("FSC-H","SSC-H","Time")])
ctrlCount<-nrow(GvHD[[1]])
sampCount<-nrow(GvHD[[16]])
stat<-calcPBChiSquare(resCtrl,resSample,ctrlCount,sampCount)

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.
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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(flowStats)
Loading required package: flowCore
Loading required package: fda
Loading required package: splines
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:flowCore':

    %&%


Attaching package: 'fda'

The following object is masked from 'package:graphics':

    matplot

Loading required package: mvoutlier
Loading required package: sgeostat
sROC 0.1-2 loaded
Loading required package: cluster
Loading required package: flowWorkspace
Loading required package: flowViz
Loading required package: lattice
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: gridExtra
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowStats/calcPBChiSquare.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calcPBChiSquare
> ### Title: Probability binning metirc for comparing the probability binned
> ###   datasets
> ### Aliases: calcPBChiSquare
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> data(GvHD)
> # flow frame 1 is treated as  control dataset and used to generate bins
> resCtrl<-proBin(GvHD[[1]][,c("FSC-H","SSC-H","Time")],200)  
> plotBins(resCtrl,GvHD[[1]],channels=c("FSC-H","SSC-H","Time"),title="Binned control data")
> # Same bins are applied to flowFrame 16
> resSample<-binByRef(resCtrl,GvHD[[16]][,c("FSC-H","SSC-H","Time")])
> ctrlCount<-nrow(GvHD[[1]])
> sampCount<-nrow(GvHD[[16]])
> stat<-calcPBChiSquare(resCtrl,resSample,ctrlCount,sampCount)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>