ProbBin.FCS {rflowcyt}R Documentation

ProbBin.FCS R-object: Probability binning of 2 samples

Description

Constructs a list of histogram objects and other variables on the probability binning between 2 samples, usually the stimulated and unstimulated data (post gating).

Usage


ProbBin.FCS(controldata, stimuldata, N, varname = "",
PBspec = c("by.control", "combined"), MY.DEBUG = TRUE, ...)

Arguments

controldata a vector of the unstimulated sample data (of 1 variable)
stimuldata a vector of the stimulated sample data (of 1 variable)
N the number of observations per a bin
varname character string of the name of the variable (optional)
PBspec The type of probability binning either:
"by.control"
in which the breaks for the bins are based on the unstimulated having N observations in each bin
"combined"
in which the breaks for the bins are based on the combined dataset (stimulated and unstimulated) having N observations in each bin
MY.DEBUG If TRUE, then debugging statements will be printed; default is TRUE.
... other options besides 'plot' and 'br' in hist function

Details

Based on either the control data or the combined data, breaks for the bins are determined by having a specific number of observations fall in each bin. These breaks are then applied to the stimulated data or both the control and stimulated data, respectively. The resulting two histograms (one of the stimulated data and the other of the control data) are the result of this probability binning method.

Value

unst.hist histogram object of the control/unstimulated data
st.hist histogram object of the stimulated data
PB type of Probability binning: either "by.control" or "combined"
N.in.bin number in each bin
varname character string of the variable name

WARNING

Gating and subsetting should precede the analysis and the use of this function. It is a good idea to implement icreateGate or createGate and extractGatedData before this analysis on univariate data.

Note

Further graphing & testing can be implemented via the following functions in rflowcyt package:plot.ProbBin.FCS, summary.ProbBin.FCS, ProbBin.flowcytest

Author(s)

Zoe Moodie, A.J. Rossini, J.Y. Wan

References

Mario Roederer, et al. "Probability Binning Comparison: A Metric for Quantitating Univariate Distribution Differences" Cytometry 45:37-46 (2001).

See Also

hist, breakpoints.ProbBin, plot.ProbBin.FCS, summary.ProbBin.FCS, ProbBin.flowcytest, is, as

Examples


if (require(rfcdmin)){

data.there<-is.element(c("st.1829", "unst.1829", "st.DRT", "unst.DRT"),objects())
if ( ( sum(data.there) != length(data.there) )){
## obtaining the FCS objects from VRC data
data(VRCmin)
}
## This only serves as an example.
## Gating/subsetting should precede this analysis
IFN.gamma.1<-unst.1829@data[1:2000,4]
IFN.gamma.2<-st.1829@data[1:2000,4]

#Probability binning using the control dataset to determine the breaks
PB1<-ProbBin.FCS(IFN.gamma.1, IFN.gamma.2, 200,
varname=colnames(unst.1829@data)[4], PBspec="by.control",MY.DEBUG=FALSE)

## Probability Binning using the combined dataset (control & stimulated)
## to determing the breaks
PB2<-ProbBin.FCS(IFN.gamma.1, IFN.gamma.2, 200,
varname=colnames(unst.1829@data)[4], PBspec="combined",MY.DEBUG=FALSE)
}


[Package rflowcyt version 1.4.0 Index]