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