.classifyDfOnChannel    K-means classify a data frame where the
                        droplets are negative in the same channels
                        only.
.classifyOnChannel      K-means classify a list of data frames
                        individually, where each data frame comprises
                        droplets that are negative in the same channels
                        only.
.classwiseMahalanobisRain
                        Fuzzy clusters by bivariate normal
                        distributions.
.cov                    Get the covariance of a cluster.
.dependentCols          Get a vector of all dependent columns.
.essentialDependentCols
                        Get a vector of essential dependent columns.
.extractWellNames       Retrieve the well names to use from a given
                        list.
.getAllSummary          Get a summary of the number of molecules in
                        20ul.
.getChannelCentres      Find the centres of each of the wells in a
                        given channel.
.getClassificationData
                        Extract a classification from a data frame.
.getMutCopies           Get the mutant copies per 20ul of a data frame.
.getWellNames           Extract the well names from a data frame.
.getWtCopies            Get the wild type copies per 20ul of a data
                        frame.
.isTwoDimDataFrame      Checks whether an object is a data frame with
                        two leading double columns.
.isWideForm             Checks a data frame is a wide-form table.
.mahDist                Mahalanobis distance of droplets from a
                        distribution.
.matrixInverse          Get the inverse of a matrix
.numberOfWells          Find the number of wells in the data frame.
.renormaliseByChannel   Normalise a well on one channel only and then
                        transform it back to the original (combined)
                        scale.
.renormaliseWell        Normalise a well in both channels and then
                        transform it back to the original (combined)
                        scale.
.roundIt                Round to at least n decimal places.
.slice                  Splits a long vector and according to a vector
                        of sizes.
.totalCopies            Get the total number of molecules in 20ul.
KRAScounts              KRAS mutant and wild type droplet counts and
                        Poisson estimates.
KRASdata                Droplet amplitude data for KRAS mutant and wild
                        type molecules.
amplitudes              Retrieve droplet amplitudes.
basicsSummary           Get the very basic columns of a data frame.
castSummary             Makes a long form data frame into wide form.
classCov                Get the covariance of each cluster.
classMeans              Get the mean of each cluster.
classStats              Get some basic statistical properties for each
                        class.
clusterCentres          Retrieve the cluster centres.
copiesSummary           Get the total copies per 20ul of a data frame
                        in the context of the basic counts.
ddpcr                   An environment for package variables.
ddpcrPlate-class        An S4 class for multiple wells in a ddPCR
                        experiment.
ddpcrWell-class         An S4 class for the classification of a single
                        well in a ddPCR experiment.
drawBlank               Plot nothing.
dropletPlot             Plot a droplet classification with a
                        colour-blind palette, optional cluster centres
                        and fixed axes.
elementType,SimpleList-method
                        Check the types of the elements in a
                        'SimpleList'.
exportTable             Exports an object to file.
extractPlateName        Try to get plate name from a filename.
extractWellNames        Try to get well names from a vector of
                        filenames.
facetPlot               Draw each of the individual wells in a ddPCR
                        experiment.
flatPlot                Plot droplet amplitudes with all droplets
                        classified as "N/A" (or a chosen class).
fullCopiesSummary       Get all of the counts data in a summarised data
                        frame.
fullCountsSummary       Take a data frame and compute the abundance of
                        molecules.
getCutOff               Find the standard deviation of droplets (in a
                        given class) multipied by a given constant.
ggplot.well             ggplot methods for the 'ddpcrWell' and
                        'ddpcrPlate' classes.
gridClassify            Use a 'grid' to create training data for
                        classification algorithms.
heatPlot                Draw a heat plot of the droplets.
isEmpty,ddpcrWell-method
                        Is a 'ddpcrWell' object empty?
kmeansClassify          K-means classify the wells in a 'ddpcrWell' or
                        'ddpcrPlate' object, or in a data frame.
knnClassify             Use the k-nearest neighbour algorithm to
                        classify the wells in a 'ddpcrWell' or
                        'ddpcrPlate' object, or in a data frame.
mahalanobisRain         Define 'rain' (unclassified) droplets by
                        fitting the clusters to bivariate normal
                        distributions.
mutantCopiesSummary     Get the mutant copies per 20ul of a data frame
                        in the context of the basic counts.
numDroplets             Retrieve the number of droplets.
numericInputRow         Inline 'numericInputs'.
parseClusterCounts      Retain cluster counts and user-specified
                        columns in data frames.
plateClassification     Set and retrieve classifications for multiple
                        wells.
plateClassificationMethod
                        Set or retrieve the classification method
                        strings for multiple wells.
plateSummary            Counts the number of positives and negatives in
                        an experiment and produces estimates for the
                        number of molecules.
positiveCounts          Get a vector of droplet positive and negative
                        counts.
readCSVDataFrame        Read all given CSV files into a list.
relabelClasses          Re-label clusters.
removeDropletClasses    Retrieve a data frame of droplet amplitudes
                        with droplets of a given class removed.
renormalisePlate        Normalise all wells in a plate to the
                        overall/average cluster positions.
sdRain                  Add rain to a classification by using a chosen
                        multiple of standard deviation.
setChannelNames         Rename the channels.
setDropletVolume        Set the droplet volume in microlitres (ul).
shinyVis                A Shiny environment.
shinyVisApp             Shiny app.
shinyVisServer          Shiny visualisation server.
shinyVisUI              Shiny visualisation UI.
sortDataFrame           Sorts a data frame according to the well names.
sortWells               Return given well names sorted.
textInputRow            Inline 'textInputs'.
thresholdClassify       Set thresholds to classify droplets.
twoddpcr-package        Classifying and summarising 2-d droplet
                        digitial PCR (ddPCR) data.
wellClassification      Retrieve a classification vector.
wellClassificationMethod
                        Retrieve the classification method.
whiteTheme              Use a theme with a white background and grey
                        lines.
wildTypeCopiesSummary   Get the wild type copies per 20ul of a data
                        frame in the context of the basic counts.
