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. |
allPlot | Draw each of the individual wells in a ddPCR experiment. |
amplitudes | Retrieve droplet amplitudes. |
amplitudes-method | 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. |
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. |
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. |
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. |
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. |
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. |
heatPlot | Draw a heat plot of the droplets. |
heatPlot-method | Draw a heat plot of the droplets. |
isEmpty-method | Is a 'ddpcrWell' object empty? |
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. |
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. |
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. |
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. |
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. |
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. |
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. |
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. |
.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. |