calcPBChiSquare {flowStats} | 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
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)