# Statistical tools and data structures for analytic flow cytometry

## Documentation for package `rflowcyt' version 1.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C D E F G I J K L M P R S V W X misc

"addParameter-methods" | Add a column data variable to the data of a FCS object
"addParameter-methods",FCS,vector-method | Class "FCS" : Flow Cytometry Standard
"checkvars-methods" | Checks the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object.
"checkvars-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"coerce-methods" | Coercing an object class to another class
"coerce-methods",data.frame,FCS-method | Class "FCS" : Flow Cytometry Standard
"coerce-methods",FCS,data.frame-method | Class "FCS" : Flow Cytometry Standard
"coerce-methods",FCS,matrix-method | Class "FCS" : Flow Cytometry Standard
"coerce-methods",matrix,FCS-method | Class "FCS" : Flow Cytometry Standard
"dim.FCS-methods" | Obtaining the dimensions of the data of an "FCS-class" object
"dim.FCS-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"equals-methods" | Checks equality of two "FCS-class" objects
"equals-methods",FCS,FCS-method | Class "FCS" : Flow Cytometry Standard
"FCS" | Class "FCS" : Flow Cytometry Standard
"FCS-class" | Class "FCS" : Flow Cytometry Standard
"FCSgate" | Class "FCSgate" Flow Cytometry Standard extension to gating
"FCSgate-class" | Class "FCSgate" Flow Cytometry Standard extension to gating
"FCSggobi" | Class "FCSggobi" : Dynamic Plots
"FCSggobi-class" | Class "FCSggobi" : Dynamic Plots
"FCSmetadata" | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"FCSmetadata-class" | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"FCSsummary-class" | Class "FCSsummary" Summary object for a "FCS-class"
"fixvars-methods" | Checks and fixes the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object.
"fixvars-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"fluors-methods" | Obtaining the Data of Fluorescence Measurements from a FCS object
"fluors-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"ggobi-methods" | Dynamic Plotting and Viewing the "FCS" object data high-dimensionally
"ggobi-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"metaData-methods" | Extraction of the FCSmetadata-class object from a FCS-class object
"metaData-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"plot-methods" | Graphical representation of an object
"plot-methods",FCS,missing-method | Class "FCS" : Flow Cytometry Standard
"print-methods" | Printing an object
"print-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"print-methods",FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"print-methods",FCSsummary-method | Class "FCSsummary" Summary object for a "FCS-class"
"show-methods" | Showing an object
"show-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"show-methods",FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"show-methods",FCSsummary-method | Class "FCSsummary" Summary object for a "FCS-class"
"summary-methods" | Summary of object
"summary-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"summary-methods",FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"[" | Extraction of slot information using "["
"[",FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"["-methods | Extraction of slot information using "["
"[-methods" | Extraction of slot information using "["
"[-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"[-methods",FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"[<-" | Replacement and/or Addition of new slot or indexed elements using "[<-"
"[<-",FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"[<-"-methods | Replacement and/or Addition of new slot or indexed elements using "[<-"
"[<--methods" | Replacement and/or Addition of new slot or indexed elements using "[<-"
"[<--methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"[<--methods",FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"[[" | Extraction of slot information using "[["
"[[",FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"[["-methods | Extraction of slot information using "[["
"[[-methods" | Extraction of slot information using "[["
"[[-methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"[[-methods",FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"[[<-" | Replacement and/or Addition of new slot or indexed elements using "[[<-"
"[[<-"-methods | Replacement and/or Addition of new slot or indexed elements using "[[<-"
"[[<-"-methods,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
"[[<--methods" | Replacement and/or Addition of new slot or indexed elements using "[[<-"
"[[<--methods",FCS-method | Class "FCS" : Flow Cytometry Standard
"[[<--methods",FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object

## -- A --

add.parallel.coordinates | Add a parallel coordinates line to an existing plot
add.parallelCoordinates | Add a parallel coordinates line to an existing plot
addParameter | Add a column data variable to the data of a FCS object
addParameter,FCS,vector-method | Class "FCS" : Flow Cytometry Standard
addParameter-methods | Add a column data variable to the data of a FCS object

## -- B --

boxplot.FCS | Create boxplots one parameter of one (or more) FCS object(s)
breakpoints.ProbBin | Obtain break points for Probability binning

## -- C --

checkvars | Checks the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object.
checkvars,FCS-method | Class "FCS" : Flow Cytometry Standard
checkvars-methods | Checks the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object.
coerce,ANY,array-method | Coercing an object class to another class
coerce,ANY,call-method | Coercing an object class to another class
coerce,ANY,character-method | Coercing an object class to another class
coerce,ANY,complex-method | Coercing an object class to another class
coerce,ANY,environment-method | Coercing an object class to another class
coerce,ANY,expression-method | Coercing an object class to another class
coerce,ANY,function-method | Coercing an object class to another class
coerce,ANY,integer-method | Coercing an object class to another class
coerce,ANY,list-method | Coercing an object class to another class
coerce,ANY,logical-method | Coercing an object class to another class
coerce,ANY,matrix-method | Coercing an object class to another class
coerce,ANY,name-method | Coercing an object class to another class
coerce,ANY,NULL-method | Coercing an object class to another class
coerce,ANY,numeric-method | Coercing an object class to another class
coerce,ANY,single-method | Coercing an object class to another class
coerce,ANY,ts-method | Coercing an object class to another class
coerce,ANY,vector-method | Coercing an object class to another class
coerce,data.frame,FCS-method | Class "FCS" : Flow Cytometry Standard
coerce,FCS,data.frame-method | Class "FCS" : Flow Cytometry Standard
coerce,FCS,matrix-method | Class "FCS" : Flow Cytometry Standard
coerce,matrix,FCS-method | Class "FCS" : Flow Cytometry Standard
coerce-methods | Coercing an object class to another class
colnames,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
colnames<-,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
ContourScatterPlot | Image and Contour Bivariate Plot
convertS3toS4 | Converts S3 class FCS object to S4 class FCS object
createGate | Gating of a FCS object: Making a Gating/Selection index column for subsequent extraction
cytoSet-class | 'cytoSet': a class for storing raw data from a quantitative cell-based assay

## -- D --

densityplot.FCS | Create density plots one parameter of one (or more) FCS object(s)
dim.FCS | Obtaining the dimensions of the data of an "FCS-class" object
dim.FCS,ANY-method | Obtaining the dimensions of the data of an "FCS-class" object
dim.FCS,FCS-method | Class "FCS" : Flow Cytometry Standard
dim.FCS-methods | Obtaining the dimensions of the data of an "FCS-class" object

## -- E --

emp.f | Create a guassian kernel density
equals | Checks equality of two "FCS-class" objects
equals,FCS,FCS-method | Class "FCS" : Flow Cytometry Standard
equals-methods | Checks equality of two "FCS-class" objects
extractGatedData | Extract the data of a FCS object using a specified Gating Index
extractGateHistory | Extracting the gating information from the history

## -- F --

FCS | Class "FCS" : Flow Cytometry Standard
FCS-class | Class "FCS" : Flow Cytometry Standard
FCS.type | Objects providing parameters for the raw FCS file types
fcs.type | Objects providing parameters for the raw FCS file types
fcs.type.cellquest.3.1.FACS.Vantage | Objects providing parameters for the raw FCS file types
fcs.type.cellquest.3.1.FACScan | Objects providing parameters for the raw FCS file types
fcs.type.cellquest.3.3 | Objects providing parameters for the raw FCS file types
fcs.type.default | Objects providing parameters for the raw FCS file types
fcs.type.DiVa1024 | Objects providing parameters for the raw FCS file types
fcs.type.FACSCalibur1024 | Objects providing parameters for the raw FCS file types
fcs.type.facscan1024 | Objects providing parameters for the raw FCS file types
fcs.type.facscan256 | Objects providing parameters for the raw FCS file types
fcs.type.FACStar256 | Objects providing parameters for the raw FCS file types
fcs.type.LSR1024 | Objects providing parameters for the raw FCS file types
fcs.type.LSR256 | Objects providing parameters for the raw FCS file types
fcs.type.LYSYS | Objects providing parameters for the raw FCS file types
FCSgate | Class "FCSgate" Flow Cytometry Standard extension to gating
FCSgate-class | Class "FCSgate" Flow Cytometry Standard extension to gating
FCSggobi | Class "FCSggobi" : Dynamic Plots
FCSggobi-class | Class "FCSggobi" : Dynamic Plots
FCSmetadata | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
FCSmetadata-class | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
FCSsummary | Class "FCSsummary" Summary object for a "FCS-class"
FCSsummary-class | Class "FCSsummary" Summary object for a "FCS-class"
FHCRC.HVTNFCS | Fred Hutchinson Cancer Research Center Sequential Gating Procedure proposed by Julie McElrath's Lab
fixvars | Checks and fixes the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object.
fixvars,FCS-method | Class "FCS" : Flow Cytometry Standard
fixvars-methods | Checks and fixes the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object.
fluors | Obtaining the Data of Fluorescence Measurements from a FCS object
fluors,FCS-method | Class "FCS" : Flow Cytometry Standard
fluors-methods | Obtaining the Data of Fluorescence Measurements from a FCS object

## -- G --

gate.IPC | Interactive gating of an Image Parallel Coordinates Plot
get.h | Estimate the critical bandwidth for specific number of modes
get.num.modes | Number of modes of a gaussian kernel
get.p | Test if the kernel density estimate given by x and h0 has at most m modes
ggobi | Dynamic Plotting and Viewing the "FCS" object data high-dimensionally
ggobi,FCS-method | Class "FCS" : Flow Cytometry Standard
ggobi-methods | Dynamic Plotting and Viewing the "FCS" object data high-dimensionally
ggobi3.FCS | Dynamic Plotting and Viewing the "FCS" object data high-dimensionally

## -- I --

icreateGate | Gating of a FCS object: Making a Gating/Selection index column for subsequent extraction
ImageParCoord | Image Parallel Coordinates Plot: Joint and marginal

## -- J --

JointImageParCoord | Image Parallel Coordinates Plot: Joint and marginal

## -- K --

KS | Kolmogorov Smirnoff Test 2-sample

## -- L --

legend.CSP | Makes a rough legend for the ContourScatterPlot
length,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay

## -- M --

make.density | Make a matrix of values allocated in a two dimensional grid
make.grid | Make a matrix of values allocated in a two dimensional grid
metaData | Extraction of the FCSmetadata-class object from a FCS-class object
metaData,FCS-method | Class "FCS" : Flow Cytometry Standard
metaData-methods | Extraction of the FCSmetadata-class object from a FCS-class object
MODE | Estimate the highest mode of a multimodale distribution

## -- P --

pairs.CSP | Contour/Hexbin Scatterplot Matrices
parallel.coordinates | Parallel coordinates: Plotting each observation across all variables
parallelCoordinates | Parallel coordinates: Plotting each observation across all variables
pData,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
percentile.FCS | Calculate the Percent Positive given a percentile
PercentPos.FCS | Calculate the Percent Positive given a percentile
phenoData,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
phenoData<-,cytoSet,phenoData-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
pkci2 | Testing the difference of upper-tail distributions of two samples
plot,ANY,ANY-method | Graphical representation of an object
plot,FCS,missing-method | Class "FCS" : Flow Cytometry Standard
plot-methods | Graphical representation of an object
plot.ProbBin.FCS | Plots a ProbBin.FCS object
plot2sets.FCS | Create a scatterplot to summaryze and compare two series of FCS objects
plotdensity.FCS | Create density plots one parameter of one (or more) FCS object(s)
plotECDF.FCS | Create a empirical cumulative distribution plot for one (or more) parameter(s) of one (or more) FCS object(s)
plotQA.FCS | Create a scatterplot summaryzing one (or two) parameter(s) for several FCS objects stored in a plate
plotvar.FCS | Making Univariate/Bivariate plots of the column variables of a FCS object
print,ANY-method | Printing an object
print,FCS-method | Class "FCS" : Flow Cytometry Standard
print,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
print,FCSsummary-method | Class "FCSsummary" Summary object for a "FCS-class"
print-methods | Printing an object
print-methods,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
print-methods,FCSsummary-method | Class "FCSsummary" Summary object for a "FCS-class"
ProbBin.by.control | Test the equivalence of two univariate sample distributions by using Probability Binning and plots the probability-binned histograms of the two samples
ProbBin.combined | Test the equivalence of two univariate sample distributions by using Probability Binning and plots the probability-binned histograms of the two samples
ProbBin.FCS | ProbBin.FCS R-object: Probability binning of 2 samples
ProbBin.flowcytest | Test the equivalence of two univariate sample distributions by using Probability Binning and plots the probability-binned histograms of the two samples

## -- R --

read.FCS | Reading in a raw binary Flow Cytometry Standard (FCS) file
read.series.FCS | Reading a serie of raw binary Flow Cytometry Standard (FCS) files
rect.box.idx | Superimposes a rectangle on an existing plot given positional indicies
ROC.FCS | ROC (Receiver Operating Characteristic) Curve: Percentage Positives for Flow Cytometry data
runflowcytests | Tests the equivalence of two univariate sample distributions by using four different methods

## -- S --

show,ANY-method | Showing an object
show,classRepresentation-method | Showing an object
show,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
show,FCS-method | Class "FCS" : Flow Cytometry Standard
show,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
show,FCSsummary-method | Class "FCSsummary" Summary object for a "FCS-class"
show,genericFunction-method | Showing an object
show,MethodDefinition-method | Showing an object
show,MethodWithNext-method | Showing an object
show,ObjectsWithPackage-method | Showing an object
show,traceable-method | Showing an object
show-methods | Showing an object
show-methods,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
show-methods,FCSsummary-method | Class "FCSsummary" Summary object for a "FCS-class"
showgate.FCS | Showing the gate and the datapoints within the gate on a prevous plot
standard | Estimate the critical bandwidth for specific number of modes
summary,"ANY-method" | Summary of object
summary,FCS-method | Class "FCS" : Flow Cytometry Standard
summary,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
summary-methods | Summary of object
summary-methods,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
summary.ProbBin.FCS | Chi-Squared/Standard Normal Approximation Summary Statistics for a ProbBin.FCS object

## -- V --

VRC.HVTNFCS | Sequential Gating Scheme from Vaccine Research Center (VRC), NIH, Bethesda, MD; Mario Roederer, PhD

## -- W --

WLR | Weighted Logrank Test for testing the differences between time-to-event, survival curves

## -- X --

xgobi.FCS | XGobi: Dynamic Graphics for Data Analysis on FCS R objects

## -- misc --

[,ANY-method | Extraction of slot information using "["
[,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[,FCS-method | Class "FCS" : Flow Cytometry Standard
[,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
[,genericFunction-method | Extraction of slot information using "["
[-methods | Extraction of slot information using "["
[-methods,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
[<-,ANY-method | Replacement and/or Addition of new slot or indexed elements using "[<-"
[<-,FCS-method | Class "FCS" : Flow Cytometry Standard
[<-,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
[<-,genericFunction-method | Replacement and/or Addition of new slot or indexed elements using "[<-"
[<--methods | Replacement and/or Addition of new slot or indexed elements using "[<-"
[<--methods,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
[[,ANY-method | Extraction of slot information using "[["
[[,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[[,FCS-method | Class "FCS" : Flow Cytometry Standard
[[,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
[[,genericFunction-method | Extraction of slot information using "[["
[[-methods | Extraction of slot information using "[["
[[-methods,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
[[<-,ANY-method | Replacement and/or Addition of new slot or indexed elements using "[[<-"
[[<-,cytoSet-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[[<-,FCS-method | Class "FCS" : Flow Cytometry Standard
[[<-,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
[[<-,genericFunction-method | Replacement and/or Addition of new slot or indexed elements using "[[<-"
[[<--methods | Replacement and/or Addition of new slot or indexed elements using "[[<-"
[[<--methods,FCSmetadata-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object