calcPBChiSquare | R Documentation |
This function calculates the Probability binning metric proposed by
Baggerly et al. The function utilizes the data binned using the
proBin
and binByRef
functions.
calcPBChiSquare(ctrlRes,sampRes,ctrlCount,sampCount)
ctrlRes |
The result generated by calling the |
sampRes |
The result generated by calling the |
ctrlCount |
The number of events in the control sample |
sampCount |
The number of events in the test sample being compared |
A list containing the statistic, p.value, observed, expected counts and the residuals
Nishant Gopalakrishnan
proBin
, calcPBChiSquare
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)
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