Man pages for CRUKMI-ComputationalBiology/twoddpcr
Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
| amplitudes | 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. |
| clusterCentres | Retrieve the cluster centres. |
| copiesSummary | Get the total copies per 20ul of a data frame in the context... |
| ddpcr | An environment for package variables. |
| ddpcrPlate-class | An S4 class for multiple wells in a ddPCR experiment. |
| ddpcrWell-class | An S4 class for the classification of a single well in a... |
| ddpcrWell-methods | Is a 'ddpcrWell' object empty? |
| dot-classifyDfOnChannel | K-means classify a data frame where the droplets are negative... |
| dot-classifyOnChannel | K-means classify a list of data frames individually, where... |
| dot-classwiseMahalanobisRain | Fuzzy clusters by bivariate normal distributions. |
| dot-cov | Get the covariance of a cluster. |
| dot-dependentCols | Get a vector of all dependent columns. |
| dot-essentialDependentCols | Get a vector of essential dependent columns. |
| dot-extractWellNames | Retrieve the well names to use from a given list. |
| dot-getAllSummary | Get a summary of the number of molecules in 20ul. |
| dot-getChannelCentres | Find the centres of each of the wells in a given channel. |
| dot-getClassificationData | Extract a classification from a data frame. |
| dot-getMutCopies | Get the mutant copies per 20ul of a data frame. |
| dot-getWellNames | Extract the well names from a data frame. |
| dot-getWtCopies | Get the wild type copies per 20ul of a data frame. |
| dot-isTwoDimDataFrame | Checks whether an object is a data frame with two leading... |
| dot-isWideForm | Checks a data frame is a wide-form table. |
| dot-mahDist | Mahalanobis distance of droplets from a distribution. |
| dot-matrixInverse | Get the inverse of a matrix |
| dot-numberOfWells | Find the number of wells in the data frame. |
| dot-renormaliseByChannel | Normalise a well on one channel only and then transform it... |
| dot-renormaliseWell | Normalise a well in both channels and then transform it back... |
| dot-roundIt | Round to at least n decimal places. |
| dot-slice | Splits a long vector and according to a vector of sizes. |
| dot-totalCopies | Get the total number of molecules in 20ul. |
| drawBlank | Plot nothing. |
| dropletPlot | Plot a droplet classification with a colour-blind palette,... |
| elementType-SimpleList-method | Check the types of the elements in a 'SimpleList'. |
| exportTable | 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. |
| flatPlot | Plot droplet amplitudes with all droplets classified as "N/A"... |
| 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)... |
| ggplot.well | ggplot methods for the 'ddpcrWell' and 'ddpcrPlate' classes. |
| gridClassify | Use a 'grid' to create training data for classification... |
| heatPlot | Draw a heat plot of the droplets. |
| kmeansClassify | K-means classify the wells in a 'ddpcrWell' or 'ddpcrPlate'... |
| knnClassify | Use the k-nearest neighbour algorithm to classify the wells... |
| KRAScounts | KRAS mutant and wild type droplet counts and Poisson... |
| KRASdata | Droplet amplitude data for KRAS mutant and wild type... |
| mahalanobisRain | Define 'rain' (unclassified) droplets by fitting the clusters... |
| mutantCopiesSummary | Get the mutant copies per 20ul of a data frame in the context... |
| numDroplets | Retrieve the number of droplets. |
| numericInputRow | Inline 'numericInputs'. |
| parseClusterCounts | Retain cluster counts and user-specified columns in data... |
| plateClassification | Set and retrieve classifications for multiple wells. |
| plateClassificationMethod | Set or retrieve the classification method strings for... |
| plateSummary | Counts the number of positives and negatives in an 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... |
| renormalisePlate | Normalise all wells in a plate to the overall/average cluster... |
| sdRain | Add rain to a classification by using a chosen multiple of... |
| setChannelNames | Rename the channels. |
| setDropletVolume | Set the droplet volume in microlitres (ul). |
| shinyVis | A Shiny environment. |
| shinyVisApp | Shiny app. |
| shinyVisServer | Shiny visualisation server. |
| shinyVisUI | Shiny visualisation UI. |
| 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. |
| twoddpcr-package | Classifying and summarising 2-d droplet digitial PCR (ddPCR)... |
| wellClassification | Retrieve a classification vector. |
| wellClassificationMethod | 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... |
