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

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Documentation for package ‘twoddpcr’ version 1.11.0

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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.