ProbBin.FCS {rflowcyt} | R Documentation |
Constructs a list of histogram objects and other variables on the probability binning between 2 samples, usually the stimulated and unstimulated data (post gating).
ProbBin.FCS(controldata, stimuldata, N, varname = "", PBspec = c("by.control", "combined"), MY.DEBUG = TRUE, ...)
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:
|
MY.DEBUG |
If TRUE, then debugging statements will be printed; default is TRUE. |
... |
other options besides 'plot' and 'br' in hist function |
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.
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 |
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.
Further graphing & testing can be implemented via the following functions in
rflowcyt package:plot.ProbBin.FCS
,
summary.ProbBin.FCS
, ProbBin.flowcytest
Zoe Moodie, A.J. Rossini, J.Y. Wan
Mario Roederer, et al. "Probability Binning Comparison: A Metric for Quantitating Univariate Distribution Differences" Cytometry 45:37-46 (2001).
hist
, breakpoints.ProbBin
, plot.ProbBin.FCS
,
summary.ProbBin.FCS
, ProbBin.flowcytest
,
is
, as
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) }