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

amplitudesRetrieve droplet amplitudes.
basicsSummaryGet the very basic columns of a data frame.
castSummaryMakes a long form data frame into wide form.
classCovGet the covariance of each cluster.
classMeansGet the mean of each cluster.
classStatsGet some basic statistical properties for each class.
clusterCentresRetrieve the cluster centres.
copiesSummaryGet the total copies per 20ul of a data frame in the context...
ddpcrAn environment for package variables.
ddpcrPlate-classAn S4 class for multiple wells in a ddPCR experiment.
ddpcrWell-classAn S4 class for the classification of a single well in a...
ddpcrWell-methodsIs a 'ddpcrWell' object empty?
drawBlankPlot nothing.
dropletPlotPlot a droplet classification with a colour-blind palette,...
elementType-SimpleList-methodCheck the types of the elements in a 'SimpleList'.
exportTableExports an object to file.
extractPlateNameTry to get plate name from a filename.
extractWellNamesTry to get well names from a vector of filenames.
facetPlotDraw each of the individual wells in a ddPCR experiment.
flatPlotPlot droplet amplitudes with all droplets classified as "N/A"...
fullCopiesSummaryGet all of the counts data in a summarised data frame.
fullCountsSummaryTake a data frame and compute the abundance of molecules.
getCutOffFind the standard deviation of droplets (in a given class)...
ggplot.wellggplot methods for the 'ddpcrWell' and 'ddpcrPlate' classes.
gridClassifyUse a 'grid' to create training data for classification...
heatPlotDraw a heat plot of the droplets.
kmeansClassifyK-means classify the wells in a 'ddpcrWell' or 'ddpcrPlate'...
knnClassifyUse the k-nearest neighbour algorithm to classify the wells...
KRAScountsKRAS mutant and wild type droplet counts and Poisson...
KRASdataDroplet amplitude data for KRAS mutant and wild type...
mahalanobisRainDefine 'rain' (unclassified) droplets by fitting the clusters...
mutantCopiesSummaryGet the mutant copies per 20ul of a data frame in the context...
numDropletsRetrieve the number of droplets.
numericInputRowInline 'numericInputs'.
parseClusterCountsRetain cluster counts and user-specified columns in data...
plateClassificationSet and retrieve classifications for multiple wells.
plateClassificationMethodSet or retrieve the classification method strings for...
plateSummaryCounts the number of positives and negatives in an experiment...
positiveCountsGet a vector of droplet positive and negative counts.
readCSVDataFrameRead all given CSV files into a list.
relabelClassesRe-label clusters.
removeDropletClassesRetrieve a data frame of droplet amplitudes with droplets of...
renormalisePlateNormalise all wells in a plate to the overall/average cluster...
sdRainAdd rain to a classification by using a chosen multiple of...
setChannelNamesRename the channels.
setDropletVolumeSet the droplet volume in microlitres (ul).
shinyVisA Shiny environment.
shinyVisAppShiny app.
shinyVisServerShiny visualisation server.
shinyVisUIShiny visualisation UI.
sortDataFrameSorts a data frame according to the well names.
sortWellsReturn given well names sorted.
textInputRowInline 'textInputs'.
thresholdClassifySet thresholds to classify droplets.
twoddpcr-packageClassifying and summarising 2-d droplet digitial PCR (ddPCR)...
wellClassificationRetrieve a classification vector.
wellClassificationMethodRetrieve the classification method.
whiteThemeUse a theme with a white background and grey lines.
wildTypeCopiesSummaryGet the wild type copies per 20ul of a data frame in the...
twoddpcr documentation built on Nov. 17, 2017, 1:11 p.m.