Entry: ContourScatterPlot
Aliases: ContourScatterPlot
Keywords: hplot
Description: Image and Contour Bivariate Plot
URL: ../../../library/rflowcyt/html/ContourScatterPlot.html

Entry: "FCS-class"
Aliases: "FCS" FCS-class FCS "FCS-class" [,FCS-method [<-,FCS-method [[,FCS-method [[<-,FCS-method "[-methods",FCS-method "[<--methods",FCS-method "[[-methods",FCS-method "[[<--methods",FCS-method addParameter,FCS,vector-method checkvars,FCS-method coerce,FCS,matrix-method coerce,FCS,data.frame-method coerce,matrix,FCS-method coerce,data.frame,FCS-method dim.FCS,FCS-method equals,FCS,FCS-method fixvars,FCS-method fluors,FCS-method ggobi,FCS-method metaData,FCS-method plot,FCS,missing-method print,FCS-method show,FCS-method summary,FCS-method "addParameter-methods",FCS,vector-method "checkvars-methods",FCS-method "coerce-methods",FCS,matrix-method "coerce-methods",FCS,data.frame-method "coerce-methods",matrix,FCS-method "coerce-methods",data.frame,FCS-method "dim.FCS-methods",FCS-method "equals-methods",FCS,FCS-method "fixvars-methods",FCS-method "fluors-methods",FCS-method "ggobi-methods",FCS-method "metaData-methods",FCS-method "plot-methods",FCS,missing-method "print-methods",FCS-method "show-methods",FCS-method "summary-methods",FCS-method
Keywords: classes
Description: Class "FCS" : Flow Cytometry Standard
URL: ../../../library/rflowcyt/html/FCS-class.html

Entry: "FCSgate-class"
Aliases: "FCSgate-class" "FCSgate" FCSgate-class FCSgate
Keywords: classes
Description: Class "FCSgate" Flow Cytometry Standard extension to gating
URL: ../../../library/rflowcyt/html/FCSgate-class.html

Entry: "FCSggobi-class"
Aliases: "FCSggobi-class" "FCSggobi" FCSggobi-class FCSggobi
Keywords: classes
Description: Class "FCSggobi" : Dynamic Plots
URL: ../../../library/rflowcyt/html/FCSggobi-class.html

Entry: "FCSmetadata-class"
Aliases: "FCSmetadata-class" "FCSmetadata" FCSmetadata-class FCSmetadata "[-methods",FCSmetadata-method "[<--methods",FCSmetadata-method "[[-methods",FCSmetadata-method "[[<--methods",FCSmetadata-method "print-methods",FCSmetadata-method "show-methods",FCSmetadata-method "summary-methods",FCSmetadata-method "[",FCSmetadata-method "[<-",FCSmetadata-method "[[",FCSmetadata-method "[[<-"-methods,FCSmetadata-method [-methods,FCSmetadata-method [<--methods,FCSmetadata-method [[-methods,FCSmetadata-method [[<--methods,FCSmetadata-method print-methods,FCSmetadata-method show-methods,FCSmetadata-method summary-methods,FCSmetadata-method [,FCSmetadata-method [<-,FCSmetadata-method [[,FCSmetadata-method [[<-,FCSmetadata-method print,FCSmetadata-method show,FCSmetadata-method summary,FCSmetadata-method
Keywords: classes
Description: Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
URL: ../../../library/rflowcyt/html/FCSmetadata-class.html

Entry: "FCSsummary-class"
Aliases: "FCSsummary-class" FCSsummary-class FCSsummary "print-methods",FCSsummary-method "show-methods",FCSsummary-method print-methods,FCSsummary-method show-methods,FCSsummary-method print,FCSsummary-method show,FCSsummary-method
Keywords: classes
Description: Class "FCSsummary" Summary object for a "FCS-class"
URL: ../../../library/rflowcyt/html/FCSsummary-class.html

Entry: FHCRC.HVTNFCS
Aliases: FHCRC.HVTNFCS
Keywords: iplot
Description: Fred Hutchinson Cancer Research Center Sequential Gating Procedure proposed by Julie McElrath's Lab
URL: ../../../library/rflowcyt/html/FHCRC.HVTNFCS.html

Entry: ImageParCoord
Aliases: ImageParCoord JointImageParCoord
Keywords: hplot
Description: Image Parallel Coordinates Plot: Joint and marginal
URL: ../../../library/rflowcyt/html/ImageParCoord.html

Entry: KS.flowcytest
Aliases: KS.flowcytest KS
Keywords: dplot distribution
Description: Kolmogorov Smirnoff Test 2-sample
URL: ../../../library/rflowcyt/html/KS.flowcytest.html

Entry: MODE
Aliases: MODE
Keywords: distribution
Description: Estimate the highest mode of a multimodale distribution
URL: ../../../library/rflowcyt/html/MODE.html

Entry: PercentPos.FCS
Aliases: PercentPos.FCS percentile.FCS
Keywords: dplot math
Description: Calculate the Percent Positive given a percentile
URL: ../../../library/rflowcyt/html/PercentPos.FCS.html

Entry: ProbBin.FCS
Aliases: ProbBin.FCS
Keywords: univar classes
Description: ProbBin.FCS R-object: Probability binning of 2 samples
URL: ../../../library/rflowcyt/html/ProbBin.FCS.html

Entry: ProbBin.flowcytest
Aliases: ProbBin.flowcytest ProbBin.by.control ProbBin.combined
Keywords: univar hplot
Description: Test the equivalence of two univariate sample distributions by using Probability Binning and plots the probability-binned histograms of the two samples
URL: ../../../library/rflowcyt/html/ProbBin.flowcytest.html

Entry: ROC.FCS
Aliases: ROC.FCS
Keywords: dplot aplot
Description: ROC (Receiver Operating Characteristic) Curve: Percentage Positives for Flow Cytometry data
URL: ../../../library/rflowcyt/html/ROC.FCS.html

Entry: VRC.HVTNFCS
Aliases: VRC.HVTNFCS
Keywords: iplot
Description: Sequential Gating Scheme from Vaccine Research Center (VRC), NIH, Bethesda, MD; Mario Roederer, PhD
URL: ../../../library/rflowcyt/html/VRC.HVTNFCS.html

Entry: WLR.flowcytest
Aliases: WLR.flowcytest WLR
Keywords: survival univar hplot
Description: Weighted Logrank Test for testing the differences between time-to-event, survival curves
URL: ../../../library/rflowcyt/html/WLR.flowcytest.html

Entry: add.parallel.coordinates
Aliases: add.parallel.coordinates
Keywords: hplot
Description: Add a parallel coordinates line to an existing plot
URL: ../../../library/rflowcyt/html/add.parallel.coordinates.html

Entry: add.parallelCoordinates
Aliases: add.parallelCoordinates
Keywords: hplot
Description: Add a parallel coordinates line to an existing plot
URL: ../../../library/rflowcyt/html/add.parallelCoordinates.html

Entry: "addParameter-methods"
Aliases: "addParameter-methods" addParameter-methods addParameter
Keywords: methods data manip
Description: Add a column data variable to the data of a FCS object
URL: ../../../library/rflowcyt/html/addParameter-methods.html

Entry: boxplot.FCS
Aliases: boxplot.FCS
Keywords: aplot
Description: Create boxplots one parameter of one (or more) FCS object(s)
URL: ../../../library/rflowcyt/html/boxplot.FCS.html

Entry: breakpoints.ProbBin
Aliases: breakpoints.ProbBin
Keywords: dplot
Description: Obtain break points for Probability binning
URL: ../../../library/rflowcyt/html/breakpoints.ProbBin.html

Entry: "checkvars-methods"
Aliases: "checkvars-methods" checkvars-methods checkvars
Keywords: methods data
Description: Checks the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object.
URL: ../../../library/rflowcyt/html/checkvars-methods.html

Entry: coerce-FCSformat
Aliases: coerce,FCS,cytoFrame-method coerce,cytoFrame,FCS-method
Keywords: classes data
Description: Convert Data Objects
URL: ../../../library/rflowcyt/html/coerce-FCSformat.html

Entry: "coerce-methods"
Aliases: "coerce-methods" coerce-methods coerce,ANY,array-method coerce,ANY,call-method coerce,ANY,character-method coerce,ANY,complex-method coerce,ANY,environment-method coerce,ANY,expression-method coerce,ANY,function-method coerce,ANY,integer-method coerce,ANY,list-method coerce,ANY,logical-method coerce,ANY,matrix-method coerce,ANY,name-method coerce,ANY,numeric-method coerce,ANY,single-method coerce,ANY,ts-method coerce,ANY,vector-method coerce,ANY,NULL-method
Keywords: methods
Description: Coercing an object class to another class
URL: ../../../library/rflowcyt/html/coerce-methods.html

Entry: convertS3toS4
Aliases: convertS3toS4
Keywords: classes character
Description: Converts S3 class FCS object to S4 class FCS object
URL: ../../../library/rflowcyt/html/convertS3toS4.html

Entry: createGate
Aliases: createGate icreateGate
Keywords: iplot manip data
Description: Gating of a FCS object: Making a Gating/Selection index column for subsequent extraction
URL: ../../../library/rflowcyt/html/createGate.html

Entry: cytoSet-class
Aliases: cytoSet-class [,cytoSet-method [[,cytoSet-method [[<-,cytoSet-method show,cytoSet-method length,cytoSet-method pData,cytoSet-method colnames,cytoSet-method colnames<-,cytoSet-method phenoData,cytoSet-method phenoData<-,cytoSet,phenoData-method
Keywords: classes
Description: 'cytoSet': a class for storing raw data from a quantitative cell-based assay
URL: ../../../library/rflowcyt/html/cytoSet-class.html

Entry: "dim.FCS-methods"
Aliases: "dim.FCS-methods" dim.FCS-methods dim.FCS,ANY-method dim.FCS
Keywords: methods
Description: Obtaining the dimensions of the data of an "FCS-class" object
URL: ../../../library/rflowcyt/html/dim.FCS-methods.html

Entry: emp.f
Aliases: emp.f
Keywords: distribution
Description: Create a guassian kernel density
URL: ../../../library/rflowcyt/html/emp.f.html

Entry: "equals-methods"
Aliases: "equals-methods" equals-methods equals
Keywords: methods data
Description: Checks equality of two "FCS-class" objects
URL: ../../../library/rflowcyt/html/equals-methods.html

Entry: extractGateHistory
Aliases: extractGateHistory
Keywords: data manip
Description: Extracting the gating information from the history
URL: ../../../library/rflowcyt/html/extractGateHistory.html

Entry: extractGatedData
Aliases: extractGatedData
Keywords: data manip
Description: Extract the data of a FCS object using a specified Gating Index
URL: ../../../library/rflowcyt/html/extractGatedData.html

Entry: fcs.type
Aliases: fcs.type FCS.type fcs.type.LYSYS fcs.type.cellquest.3.1.FACS.Vantage fcs.type.cellquest.3.1.FACScan fcs.type.cellquest.3.3 fcs.type.default fcs.type.LSR256 fcs.type.FACStar256 fcs.type.facscan256 fcs.type.DiVa1024 fcs.type.FACSCalibur1024 fcs.type.LSR1024 fcs.type.facscan1024
Keywords: environment
Description: Objects providing parameters for the raw FCS file types
URL: ../../../library/rflowcyt/html/fcs.type.html

Entry: "fixvars-methods"
Aliases: "fixvars-methods" fixvars-methods fixvars
Keywords: methods data
Description: Checks and fixes the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object.
URL: ../../../library/rflowcyt/html/fixvars-methods.html

Entry: "fluors-methods"
Aliases: "fluors-methods" fluors-methods fluors
Keywords: methods
Description: Obtaining the Data of Fluorescence Measurements from a FCS object
URL: ../../../library/rflowcyt/html/fluors-methods.html

Entry: gate.IPC
Aliases: gate.IPC
Keywords: hplot
Description: Interactive gating of an Image Parallel Coordinates Plot
URL: ../../../library/rflowcyt/html/gate.IPC.html

Entry: get.h
Aliases: get.h
Keywords: distribution
Description: Estimate the critical bandwidth for specific number of modes
URL: ../../../library/rflowcyt/html/get.h.html

Entry: get.num.modes
Aliases: get.num.modes
Keywords: distribution
Description: Number of modes of a gaussian kernel
URL: ../../../library/rflowcyt/html/get.num.modes.html

Entry: get.p
Aliases: get.p
Keywords: distribution
Description: Test if the kernel density estimate given by x and h0 has at most m modes
URL: ../../../library/rflowcyt/html/get.p.html

Entry: "ggobi-methods"
Aliases: "ggobi-methods" ggobi-methods ggobi ggobi3.FCS
Keywords: methods hplot
Description: Dynamic Plotting and Viewing the "FCS" object data high-dimensionally
URL: ../../../library/rflowcyt/html/ggobi-methods.html

Entry: legend.CSP
Aliases: legend.CSP
Keywords: hplot
Description: Makes a rough legend for the ContourScatterPlot
URL: ../../../library/rflowcyt/html/legend.CSP.html

Entry: make.grid
Aliases: make.density make.grid
Keywords: manip hplot
Description: Make a matrix of values allocated in a two dimensional grid
URL: ../../../library/rflowcyt/html/make.grid.html

Entry: "metaData-methods"
Aliases: "metaData-methods" metaData-methods metaData
Keywords: methods
Description: Extraction of the FCSmetadata-class object from a FCS-class object
URL: ../../../library/rflowcyt/html/metaData-methods.html

Entry: pairs.CSP
Aliases: pairs.CSP
Keywords: hplot
Description: Contour/Hexbin Scatterplot Matrices
URL: ../../../library/rflowcyt/html/pairs.CSP.html

Entry: parallel.coordinates
Aliases: parallel.coordinates
Keywords: hplot
Description: Parallel coordinates: Plotting each observation across all variables
URL: ../../../library/rflowcyt/html/parallel.coordinates.html

Entry: parallelCoordinates
Aliases: parallelCoordinates
Keywords: hplot
Description: Parallel coordinates: Plotting each observation across all variables
URL: ../../../library/rflowcyt/html/parallelCoordinates.html

Entry: pkci2.flowcytest
Aliases: pkci2.flowcytest pkci2
Keywords: univar htest
Description: Testing the difference of upper-tail distributions of two samples
URL: ../../../library/rflowcyt/html/pkci2.flowcytest.html

Entry: "plot-methods"
Aliases: "plot-methods" plot-methods plot,ANY,ANY-method
Keywords: methods hplot
Description: Graphical representation of an object
URL: ../../../library/rflowcyt/html/plot-methods.html

Entry: plot.ProbBin.FCS
Aliases: plot.ProbBin.FCS
Keywords: hplot
Description: Plots a ProbBin.FCS object
URL: ../../../library/rflowcyt/html/plot.ProbBin.FCS.html

Entry: plot2sets.FCS
Aliases: plot2sets.FCS
Keywords: hplot
Description: Create a scatterplot to summaryze and compare two series of FCS objects
URL: ../../../library/rflowcyt/html/plot2sets.FCS.html

Entry: plotECDF.FCS
Aliases: plotECDF.FCS
Keywords: hplot
Description: Create a empirical cumulative distribution plot for one (or more) parameter(s) of one (or more) FCS object(s)
URL: ../../../library/rflowcyt/html/plotECDF.FCS.html

Entry: plotQA.FCS
Aliases: plotQA.FCS
Keywords: hplot
Description: Create a scatterplot summaryzing one (or two) parameter(s) for several FCS objects stored in a plate
URL: ../../../library/rflowcyt/html/plotQA.FCS.html

Entry: plotdensity.FCS
Aliases: plotdensity.FCS densityplot.FCS
Keywords: hplot
Description: Create density plots one parameter of one (or more) FCS object(s)
URL: ../../../library/rflowcyt/html/plotdensity.FCS.html

Entry: plotvar.FCS
Aliases: plotvar.FCS
Keywords: hplot
Description: Making Univariate/Bivariate plots of the column variables of a FCS object
URL: ../../../library/rflowcyt/html/plotvar.FCS.html

Entry: "print-methods"
Aliases: "print-methods" print-methods print,ANY-method
Keywords: methods data
Description: Printing an object
URL: ../../../library/rflowcyt/html/print-methods.html

Entry: read.FCS
Aliases: read.FCS
Keywords: classes character
Description: Reading in a raw binary Flow Cytometry Standard (FCS) file
URL: ../../../library/rflowcyt/html/read.FCS.html

Entry: read.series.FCS
Aliases: read.series.FCS
Keywords: classes character
Description: Reading a serie of raw binary Flow Cytometry Standard (FCS) files
URL: ../../../library/rflowcyt/html/read.series.FCS.html

Entry: rect.box.idx
Aliases: rect.box.idx
Keywords: hplot
Description: Superimposes a rectangle on an existing plot given positional indicies
URL: ../../../library/rflowcyt/html/rect.box.idx.html

Entry: rflowcyt-defunct
Aliases: rflowcyt-defunct
Keywords: error
Description: Defunct Functions in rflowcyt package
URL: ../../../library/rflowcyt/html/rflowcyt-defunct.html

Entry: runflowcytests
Aliases: runflowcytests
Keywords: univar dplot hplot
Description: Tests the equivalence of two univariate sample distributions by using four different methods
URL: ../../../library/rflowcyt/html/runflowcytests.html

Entry: "show-methods"
Aliases: "show-methods" show-methods show,ANY-method show,traceable-method show,ObjectsWithPackage-method show,MethodDefinition-method show,MethodWithNext-method show,genericFunction-method show,classRepresentation-method
Keywords: methods data
Description: Showing an object
URL: ../../../library/rflowcyt/html/show-methods.html

Entry: showgate.FCS
Aliases: showgate.FCS
Keywords: aplot
Description: Showing the gate and the datapoints within the gate on a prevous plot
URL: ../../../library/rflowcyt/html/showgate.FCS.html

Entry: standard
Aliases: standard
Keywords: math
Description: Estimate the critical bandwidth for specific number of modes
URL: ../../../library/rflowcyt/html/standard.html

Entry: "[-methods"
Aliases: "[-methods" [-methods "["-methods "[" [,ANY-method [,genericFunction-method
Keywords: methods data
Description: Extraction of slot information using "["
URL: ../../../library/rflowcyt/html/subset-methods.html

Entry: "[[-methods"
Aliases: "[[-methods" [[-methods "[["-methods "[[" [[,ANY-method [[,genericFunction-method
Keywords: methods data
Description: Extraction of slot information using "[["
URL: ../../../library/rflowcyt/html/subset2-methods.html

Entry: "[[<--methods"
Aliases: "[[<--methods" [[<--methods "[[<-"-methods "[[<-" [[<-,ANY-method [[<-,genericFunction-method
Keywords: methods data
Description: Replacement and/or Addition of new slot or indexed elements using "[[<-"
URL: ../../../library/rflowcyt/html/subset2assign-methods.html

Entry: "[<--methods"
Aliases: "[<--methods" [<--methods "[<-"-methods "[<-" [<-,ANY-method [<-,genericFunction-method
Keywords: methods data
Description: Replacement and/or Addition of new slot or indexed elements using "[<-"
URL: ../../../library/rflowcyt/html/subsetassign-methods.html

Entry: "summary-methods"
Aliases: "summary-methods" summary,"ANY-method" summary-methods
Keywords: methods data
Description: Summary of object
URL: ../../../library/rflowcyt/html/summary-methods.html

Entry: summary.ProbBin.FCS
Aliases: summary.ProbBin.FCS
Keywords: univar dplot
Description: Chi-Squared/Standard Normal Approximation Summary Statistics for a ProbBin.FCS object
URL: ../../../library/rflowcyt/html/summary.ProbBin.FCS.html

Entry: xgobi.FCS
Aliases: xgobi.FCS
Keywords: hplot manip
Description: XGobi: Dynamic Graphics for Data Analysis on FCS R objects
URL: ../../../library/rflowcyt/html/xgobi.FCS.html
