calcPBChiSquare {flowStats} | R Documentation

## 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

`ctrlRes` | The result generated by calling the `probBin` function on a control dataset.
`sampRes` | The result generated by calling the `byByRef` function on a test sample dataset
`ctrlCount` | The number of events in the control sample
`sampCount` | The number of events in the test sample being compared

### Value

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

### Author(s)

Nishant Gopalakrishnan

### See Also

`proBin`, `calcPBChiSquare`

### Examples

    library(flowCore)
    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)

[Package flowStats version 4.2.0 Index]