Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules

Documentation for package ‘twoddpcr’ version 1.16.0

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Classifying and summarising 2-d droplet digitial PCR (ddPCR) data.

-- A --

allPlot	Draw each of the individual wells in a ddPCR experiment.
amplitudes	Retrieve droplet amplitudes.
amplitudes-method	Retrieve droplet amplitudes.

-- B --

basicsSummary

Get the very basic columns of a data frame.

-- C --

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.
clusterCenters	Retrieve the cluster centres.
clusterCentres	Retrieve the cluster centres.
clusterCentres-method	Retrieve the cluster centres.
combinedCenters	Retrieve the cluster centres.
combinedCentres	Retrieve the cluster centres.
combinedCentres-method	Retrieve the cluster centres.
combinedPlateCenters	Retrieve the cluster centres.
combinedPlateCentres	Retrieve the cluster centres.
commonClassificationMethod	Set or retrieve the classification method strings for multiple wells.
commonClassificationMethod-method	Set or retrieve the classification method strings for multiple wells.
copiesSummary	Get the total copies per 20ul of a data frame in the context of the basic counts.

-- D --

ddpcr	An environment for package variables.
ddpcrPlate	An S4 class for multiple wells in a ddPCR experiment.
ddpcrPlate-class	An S4 class for multiple wells in a ddPCR experiment.
ddpcrPlate-method	An S4 class for multiple wells in a ddPCR experiment.
ddpcrWell	An S4 class for the classification of a single well in a ddPCR experiment.
ddpcrWell-class	An S4 class for the classification of a single well in a ddPCR experiment.
ddpcrWell-method	An S4 class for the classification of a single well in a ddPCR experiment.
densityPlot	Draw a heat plot of the droplets.
drawBlank	Plot nothing.
dropletPlot	Plot a droplet classification with a colour-blind palette, optional cluster centres and fixed axes.
dropletPlot-method	Plot a droplet classification with a colour-blind palette, optional cluster centres and fixed axes.

-- E --

elementType-method	Check the types of the elements in a 'SimpleList'.
exportTable	Exports an object to file.
exportTable-method	Exports an object to file.
exportZip	Exports an object to file.
exportZip-method	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.

-- F --

facetPlot	Draw each of the individual wells in a ddPCR experiment.
facetPlot-method	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).
flatPlot-method	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.

-- G --

getCutOff	Find the standard deviation of droplets (in a given class) multipied by a given constant.
ggplot.multiwell	ggplot methods for the 'ddpcrWell' and 'ddpcrPlate' classes.
ggplot.plate	ggplot methods for the 'ddpcrWell' and 'ddpcrPlate' classes.
ggplot.plate-method	ggplot methods for the 'ddpcrWell' and 'ddpcrPlate' classes.
ggplot.well	ggplot methods for the 'ddpcrWell' and 'ddpcrPlate' classes.
ggplot.well-method	ggplot methods for the 'ddpcrWell' and 'ddpcrPlate' classes.
ggplot.wells	ggplot methods for the 'ddpcrWell' and 'ddpcrPlate' classes.
gridClassify	Use a 'grid' to create training data for classification algorithms.
gridClassify-method	Use a 'grid' to create training data for classification algorithms.

-- H --

heatPlot	Draw a heat plot of the droplets.
heatPlot-method	Draw a heat plot of the droplets.

-- I --

isEmpty-method

Is a 'ddpcrWell' object empty?

-- K --

kmeansClassify	K-means classify the wells in a 'ddpcrWell' or 'ddpcrPlate' object, or in a data frame.
kmeansClassify-method	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.
knnClassify-method	Use the k-nearest neighbour algorithm to classify the wells in a 'ddpcrWell' or 'ddpcrPlate' object, or in a data frame.
KRAScounts	KRAS mutant and wild type droplet counts and Poisson estimates.
KRAScountsQS	KRAS mutant and wild type droplet counts and Poisson estimates.
KRAScountsWellCol	KRAS mutant and wild type droplet counts and Poisson estimates.
KRASdata	Droplet amplitude data for KRAS mutant and wild type molecules.

-- M --

mahalanobisRain	Define 'rain' (unclassified) droplets by fitting the clusters to bivariate normal distributions.
mahalanobisRain-method	Define 'rain' (unclassified) droplets by fitting the clusters to bivariate normal distributions.
multivariateNormalRain	Define 'rain' (unclassified) droplets by fitting the clusters to bivariate normal distributions.
multivariateRain	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.
mvNormalRain	Define 'rain' (unclassified) droplets by fitting the clusters to bivariate normal distributions.
mvnRain	Define 'rain' (unclassified) droplets by fitting the clusters to bivariate normal distributions.

-- N --

numberDroplets	Retrieve the number of droplets.
numberDrops	Retrieve the number of droplets.
numberOfDroplets	Retrieve the number of droplets.
numberOfDrops	Retrieve the number of droplets.
numDroplets	Retrieve the number of droplets.
numDroplets-method	Retrieve the number of droplets.
numDrops	Retrieve the number of droplets.
numericInputRow	Inline 'numericInputs'.
numOfDroplets	Retrieve the number of droplets.

-- P --

parseClusterCounts	Retain cluster counts and user-specified columns in data frames.
plateCenters	Retrieve the cluster centres.
plateCentres	Retrieve the cluster centres.
plateClassification	Set and retrieve classifications for multiple wells.
plateClassification-method	Set and retrieve classifications for multiple wells.
plateClassification<-	Set and retrieve classifications for multiple wells.
plateClassification<--method	Set and retrieve classifications for multiple wells.
plateClassificationMethod	Set or retrieve the classification method strings for multiple wells.
plateClassificationMethod-method	Set or retrieve the classification method strings for multiple wells.
plateClassificationMethod<-	Set or retrieve the classification method strings for multiple wells.
plateClassificationMethod<--method	Set or retrieve the classification method strings for multiple wells.
plateClassificationName	Set or retrieve the classification method strings for multiple wells.
plateClassMethod	Set or retrieve the classification method strings for multiple wells.
plateClassName	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.
plateSummary-method	Counts the number of positives and negatives in an experiment and produces estimates for the number of molecules.
plotAll	Draw each of the individual wells in a ddPCR experiment.
positiveCounts	Get a vector of droplet positive and negative counts.

-- R --

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.
removeDropletClasses-method	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.

-- S --

sdRain	Add rain to a classification by using a chosen multiple of standard deviation.
sdRain-method	Add rain to a classification by using a chosen multiple of standard deviation.
setChannelNames	Rename the channels.
setChannelNames-method	Rename the channels.
setDropletVol	Set the droplet volume in microlitres (ul).
setDropletVolume	Set the droplet volume in microlitres (ul).
setDropVol	Set the droplet volume in microlitres (ul).
setDropVolume	Set the droplet volume in microlitres (ul).
shinyVis	A Shiny environment.
shinyVisApp	Shiny app.
shinyVisServer	Shiny visualisation server.
shinyVisUI	Shiny visualisation UI.
show-method	An S4 class for multiple wells in a ddPCR experiment.
show-method	An S4 class for the classification of a single well in a ddPCR experiment.
sortDataFrame	Sorts a data frame according to the well names.
sortWells	Return given well names sorted.

-- T --

textInputRow	Inline 'textInputs'.
thresholdClassify	Set thresholds to classify droplets.
thresholdClassify-method	Set thresholds to classify droplets.
twoddpcr	Classifying and summarising 2-d droplet digitial PCR (ddPCR) data.

-- W --

wellCenters	Retrieve the cluster centres.
wellCentres	Retrieve the cluster centres.
wellClassification	Retrieve a classification vector.
wellClassification-method	Retrieve a classification vector.
wellClassification<-	Retrieve a classification vector.
wellClassification<--method	Retrieve a classification vector.
wellClassificationMethod	Retrieve the classification method.
wellClassificationMethod-method	Retrieve the classification method.
wellClassificationMethod<-	Retrieve the classification method.
wellClassificationMethod<--method	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.

-- misc --

.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.
.ddpcrPlate	An S4 class for multiple wells in a ddPCR experiment.
.ddpcrWell	An S4 class for the classification of a single well in a ddPCR experiment.
.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.