Statistical tools and data structures for analytic flow cytometry


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Documentation for package ‘rflowcyt’ version 1.14.0

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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 "["
"[",ANY-method Extraction of slot information using "["
"[",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" 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 "[["
"[[",ANY-methods Extraction of slot information using "[["
"[[",genericFunction-method Extraction of slot information using "[["
"[["-method 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,cytoFrame,FCS-method Convert Data Objects
coerce,data.frame,FCS-method Class "FCS" : Flow Cytometry Standard
coerce,FCS,cytoFrame-method Convert Data Objects
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
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
rflowcyt-defunct Defunct Functions in rflowcyt package
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 --

[,cytoSet-method 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[,FCS,ANY,ANY,ANY-method Extraction of slot information using "["
[,FCS-method Class "FCS" : Flow Cytometry Standard
[,FCSmetadata,ANY,ANY,ANY-method Extraction of slot information using "["
[,FCSmetadata-method Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
[-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,ANY,ANY-method Extraction of slot information using "["
[<-,FCS-method Class "FCS" : Flow Cytometry Standard
[<-,FCSmetadata,ANY,ANY-method Extraction of slot information using "["
[<-,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
[[,cytoSet-method 'cytoSet': a class for storing raw data from a quantitative cell-based assay
[[,FCS,ANY,ANY-method Extraction of slot information using "[["
[[,FCS-method Class "FCS" : Flow Cytometry Standard
[[,FCSmetadata,ANY,ANY-method Extraction of slot information using "[["
[[,FCSmetadata-method Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object
[[-method 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, ANY, ANY Class "FCS" : Flow Cytometry Standard
[[<-,FCS,ANY,ANY-method Extraction of slot information using "[["
[[<-,FCS-method Class "FCS" : Flow Cytometry Standard
[[<-,FCSmetadata,ANY,ANY-method Extraction of slot information using "[["
[[<-,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