DebrisFilter            the Debris class
MarginEvents            the marginEvent class
PhytopFilter            the phytofilter class
accTest                 tests the accuracy of several automated gating
                        functions on monoculture flow cytometry
                        experiments.
accuracy                samples two rows in a matrix and check if the
                        samples are similar or different based on their
                        cluster labels
cellMargin              Removes or assign indicators to margin events.
clusterExtract          extract clusters based on supplied cluster
                        indicator
clusterExtractp         takes a flowframe, name of cluster column and
                        extracts part of flowframe that makes up
                        proportion.
cyanoFilter             cyanoFilter: A package to identify and cluster
                        phytoplankton cells contained in flow cytometry
                        data.
debrisNc                gates out or assign indicators to debris
                        particle based on their chlorophyll expression.
fullFlowframe           generic function for extracting the full
                        flowframe
fullFlowframe,DebrisFilter-method
                        accesor method for reduced flowframe
                        (DebrisFilter class)
fullFlowframe,MarginEvents-method
                        accesor method for the fullflowframe
                        (MarginEvent class)
fullFlowframe,PhytopFilter-method
                        accesor method for full flowframe(PhytoFilter
                        class)
gateFunc                tests the accuracy of several automated gating
                        functions on monoculture flow cytometry
                        experiments.
getChannel              returns the channel with more than one peak
                        present.  It returns NA if there is only one
                        peak present.
ggpairsDens             produces a scatter plot of the expression
                        matrix of the flowframe.  If a cluster variable
                        is given, it assigns different colors to the
                        clusters.
ggplotDens              plots two channels of a flowframe.
ggplotDens2             plots two channels of a flowframe with
                        different colors for clusters identified.
goodFcs                 indicates if measurement from a flowfile is
                        good or bad.
is.DebrisFilter         function to check if object is of class
                        cyanoFilter(DebrisFilter)
is.MarginEvents         function to check if object is of class
                        cyanoFilter(MarginEvents)
is.PhytopFilter         function to check if object is of class
                        cyanoFilter(PhytoFilter)
is.flowFrame            function to check if object is a flowFrame
is.flowSet              function to check if object is a flowSet
lnTrans                 log transforms the expression matrix of a
                        flowframe
newFlowframe            takes a flowframe, a group indicator and
                        formulates another flowframe with group
                        indicator as part of the expression matrix of
                        the new flowframe.
noNA                    Removes NA values from the expression matrix of
                        a flow cytometer file.
noNeg                   Removes negative values from the expression
                        matrix
oneDgate                returns the labels stating the cluster of each
                        row in a flowfile.
pairsPlot               produces a scatter plot of the expression
                        matrix of a flowframe. Note that, it takes some
                        time to display the plot.
phytoFilter             gates out and assign indicators to
                        phytoplankton cells based on the expression of
                        measured cell complexity channels.
pigmentGate             gates out or assign indicators to phytoplankton
                        cells based on the expression of the measured
                        pigments.
plot,DebrisFilter,ANY-method
                        plot method for DebrisFilter objects
plot,MarginEvents,ANY-method
                        plot method for MarginEvents objects
plot,PhytopFilter,ANY-method
                        plot method for PhytoFilter objects
reducedFlowframe        generic function for extracting the full
                        flowframe
reducedFlowframe,DebrisFilter-method
                        accesor method for reduced flowframe
                        (DebrisFilter class)
reducedFlowframe,MarginEvents-method
                        accesor method for reduced flowframe
                        (MarginEvent class)
reducedFlowframe,PhytopFilter-method
                        accesor method for reduced
                        flowframe(PhytoFilter class)
retain                  Decides if a file should be retiained or
                        removed based on its status.
rowNumbers              returns the position of the cells below, above
                        or between estimated gates
summaries               takes a flowframes, a vector of channels,
                        cluster indicator and return desired summaries
                        per cluster
summaries,DebrisFilter-method
                        takes a flowframes, a vector of channels,
                        cluster indicator and return desired summaries
                        per cluster
summaries,MarginEvents-method
                        takes a flowframes, a vector of channels,
                        cluster indicator and return desired summaries
                        per cluster
summaries,PhytopFilter-method
                        takes a flowframes, a vector of channels,
                        cluster indicator and return desired summaries
                        per cluster
