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

## Documentation for package ‘twoddpcr’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I K M N P R S T W misc

twoddpcr-package | 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.