A B C D E F G I J K L M P R S V W X misc
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-method | Class "FCS" : Flow Cytometry Standard |
addParameter-methods | Add a column data variable to the data of a FCS object |
boxplot.FCS | Create boxplots one parameter of one (or more) FCS object(s) |
breakpoints.ProbBin | Obtain break points for Probability binning |
checkvars | Checks the ranges, dimensions, and names of the metadata based on the current data of an FCS R-object. |
checkvars-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-method | Class "FCS" : Flow Cytometry Standard |
coerce-method | Convert Data Objects |
coerce-method | Coercing an object class to another class |
coerce-methods | Coercing an object class to another class |
colnames-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
colnames<--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 |
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-method | Class "FCS" : Flow Cytometry Standard |
dim.FCS-method | Obtaining the dimensions of the data of an "FCS-class" object |
dim.FCS-methods | Obtaining the dimensions of the data of an "FCS-class" object |
emp.f | Create a guassian kernel density |
equals | Checks equality of two "FCS-class" objects |
equals-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 |
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-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-method | Class "FCS" : Flow Cytometry Standard |
fluors-methods | Obtaining the Data of Fluorescence Measurements from a FCS object |
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-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 |
icreateGate | Gating of a FCS object: Making a Gating/Selection index column for subsequent extraction |
ImageParCoord | Image Parallel Coordinates Plot: Joint and marginal |
JointImageParCoord | Image Parallel Coordinates Plot: Joint and marginal |
KS | Kolmogorov Smirnoff Test 2-sample |
KS.flowcytest | Kolmogorov Smirnoff Test 2-sample |
legend.CSP | Makes a rough legend for the ContourScatterPlot |
length-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
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-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 |
pairs.CSP | Contour/Hexbin Scatterplot Matrices |
parallelCoordinates | Parallel coordinates: Plotting each observation across all variables |
pData-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-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
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 |
pkci2.flowcytest | Testing the difference of upper-tail distributions of two samples |
plot-method | Class "FCS" : Flow Cytometry Standard |
plot-method | Graphical representation of an object |
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-method | Class "FCS" : Flow Cytometry Standard |
print-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
print-method | Class "FCSsummary" Summary object for a "FCS-class" |
print-method | Printing an object |
print-methods | Printing an object |
print-methods-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
print-methods-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 |
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 |
show-method | Class "FCS" : Flow Cytometry Standard |
show-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
show-method | Class "FCSsummary" Summary object for a "FCS-class" |
show-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
show-method | Showing an object |
show-methods | Showing an object |
show-methods-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
show-methods-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-method | Class "FCS" : Flow Cytometry Standard |
summary-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
summary-methods | Summary of object |
summary-methods-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 |
VRC.HVTNFCS | Sequential Gating Scheme from Vaccine Research Center (VRC), NIH, Bethesda, MD; Mario Roederer, PhD |
WLR | Weighted Logrank Test for testing the differences between time-to-event, survival curves |
WLR.flowcytest | Weighted Logrank Test for testing the differences between time-to-event, survival curves |
xgobi.FCS | XGobi: Dynamic Graphics for Data Analysis on FCS R objects |
"addParameter-methods" | Add a column data variable to the data of a FCS object |
"addParameter-methods"-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"-method | Class "FCS" : Flow Cytometry Standard |
"coerce-methods" | Coercing an object class to another class |
"coerce-methods"-method | Class "FCS" : Flow Cytometry Standard |
"dim.FCS-methods" | Obtaining the dimensions of the data of an "FCS-class" object |
"dim.FCS-methods"-method | Class "FCS" : Flow Cytometry Standard |
"equals-methods" | Checks equality of two "FCS-class" objects |
"equals-methods"-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"-method | Class "FCS" : Flow Cytometry Standard |
"fluors-methods" | Obtaining the Data of Fluorescence Measurements from a FCS object |
"fluors-methods"-method | Class "FCS" : Flow Cytometry Standard |
"ggobi-methods" | Dynamic Plotting and Viewing the "FCS" object data high-dimensionally |
"ggobi-methods"-method | Class "FCS" : Flow Cytometry Standard |
"metaData-methods" | Extraction of the FCSmetadata-class object from a FCS-class object |
"metaData-methods"-method | Class "FCS" : Flow Cytometry Standard |
"plot-methods" | Graphical representation of an object |
"plot-methods"-method | Class "FCS" : Flow Cytometry Standard |
"print-methods" | Printing an object |
"print-methods"-method | Class "FCS" : Flow Cytometry Standard |
"print-methods"-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
"print-methods"-method | Class "FCSsummary" Summary object for a "FCS-class" |
"show-methods" | Showing an object |
"show-methods"-method | Class "FCS" : Flow Cytometry Standard |
"show-methods"-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
"show-methods"-method | Class "FCSsummary" Summary object for a "FCS-class" |
"summary-methods" | Summary of object |
"summary-methods"-method | Class "FCS" : Flow Cytometry Standard |
"summary-methods"-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
"[" | Extraction of slot information using "[" |
"["-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
"["-method | Extraction of slot information using "[" |
"["-methods | Extraction of slot information using "[" |
"[-methods" | Extraction of slot information using "[" |
"[-methods"-method | Class "FCS" : Flow Cytometry Standard |
"[-methods"-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
"[<-" | Replacement and/or Addition of new slot or indexed elements using "[<-" |
"[<-"-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"-method | Class "FCS" : Flow Cytometry Standard |
"[<--methods"-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
"[[" | Extraction of slot information using "[[" |
"[[",ANY-methods | Extraction of slot information using "[[" |
"[["-method | Extraction of slot information using "[[" |
"[[-methods" | Extraction of slot information using "[[" |
"[[-methods"-method | Class "FCS" : Flow Cytometry Standard |
"[[-methods"-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-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
"[[<--methods" | Replacement and/or Addition of new slot or indexed elements using "[[<-" |
"[[<--methods"-method | Class "FCS" : Flow Cytometry Standard |
"[[<--methods"-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
[-method | Class "FCS" : Flow Cytometry Standard |
[-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
[-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
[-method | Extraction of slot information using "[" |
[-methods | Extraction of slot information using "[" |
[-methods-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
[<--method | Class "FCS" : Flow Cytometry Standard |
[<--method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
[<--method | Extraction of slot information using "[" |
[<--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-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
[[-method | Class "FCS" : Flow Cytometry Standard |
[[-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
[[-method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
[[-method | Extraction of slot information using "[[" |
[[-methods-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
[[<-,FCS, ANY, ANY | Class "FCS" : Flow Cytometry Standard |
[[<--method | Class "FCS" : Flow Cytometry Standard |
[[<--method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |
[[<--method | 'cytoSet': a class for storing raw data from a quantitative cell-based assay |
[[<--method | Extraction of slot information using "[[" |
[[<--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-method | Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard object |