Man pages for jsemple19/EMclassifieR
Classify DSMF data using the Expectation Maximisation algorithm
| allClassMeansToGR | Convert allClassMeans table to GenomicRanges |
| canberraDist | Calculate canberra distance between all rows of a matrix |
| classifyAndSortReads | Classify and sort reads into their classes |
| classLikelihoodPerRead | Get likelihood of different classes for each read |
| clusterRandomMatrices | Estimate within cluster sum of squares |
| combineSilStats | Combine read counts in each class from silStats files |
| correlationDist | Calculate correlation distance between all rows of a matrix |
| cosineDist | Calculate cosine distance between all rows of a matrix |
| countGenesPerClass | Count genes per class |
| doSingleUMAPplot | Plot UMAP of data matrix |
| em_basic | Expectation Maximisation algorithm |
| em_classify | Expectation Maximisation algorithm |
| euclideanDist | Calculate euclidean distance between all rows of a matrix |
| getAllClassMeansMatrix | Collect all the class means from allClassMeans object |
| getClassMeansMatrix | Get a matrix of class mean profiles from allCalssMeans table |
| getClassVote | Get most frequently assigned class from repeat runs |
| getDistMatrix | A generic function for implementing various distance metrics |
| getFullMatrix | Get full matrix of all positions in a window even if no C |
| getMode | Get mode (most frequent value) |
| getReadClass | Extract class info from dataOrderedByClass |
| getSilhouetteStats | Draw silhouette plots and get silhouette statistics |
| isMatrixValid | Test if matrix is valid |
| makeDirs | Make directories |
| miDist | Calculate mutual information distance between all rows of a... |
| order_by_prev_cluster | Order classes |
| padEndToRange | Pad end of matrix with missing columns |
| padMissingColWithNAs | Add padding between informative positions. |
| p_converged | Check if p value has converged |
| p_difference | Get absolute value of difference between two p values |
| plotAllClassMeans | Plot all class means from multiple repeats |
| plotClassesSingleMolecule | Plot reads by class for a single gene |
| plotClassMeans | Plot class Means |
| plotClassMeansWithTracks | Plot smoothed class means from multiple repeats |
| plotClassStability | Plot histograms of consistency of classfiications over... |
| plotClusteringMetrics | Plot clustering metrics |
| plotEachRepeat | Plot single molecule and class means for individual repeats |
| plotFinalClasses | Plot reads and class means with final classification |
| plotGenesPerClass | Plot number of genes per class |
| plotMatPCA | Plot pca of data matrix |
| plotMatUMAP | Plot UMAP of data matrix |
| plotPCAofMatrixClasses | Plot PCAs of matricies for different classifications |
| plotSmoothedClassMeans | Plot smoothed class means from multiple repeats |
| plotUMAPofMatrixClasses | Plot UMAP for different classifications |
| prepareWindows | Make window matrix |
| randomiseMatrixRows | Randomise the values in each row of a matrix |
| recodeMatrixAsNumeric | Recode matrix |
| reexports | import dopar function |
| remove0 | Remove the number 0 from a vector |
| removeNArows | Remove rows containing NAs |
| rescale_0To1 | Recode matrix |
| rescale_minus1To1 | Recode matrix |
| runClassLikelihoodRpts | Run several repeats classifying reads into classes |
| runEM | Run EM iteratively to convergence |
| runEMrangeClassNum | Run EM to predict a range of class numbers |
| runEMrepeats | Run several repeats of iterative EM |
| runEMrepeats_withinSS | Run several repeats of iterative EM for randomised data |
| selectReadsFromMatrix | Select reads from multiple genes |
| silhouettePlot | Plot silhouette plot to evaluate classification |
| SumSqMatrixRows | Calculate the sum of square distances between rows of a... |
| withinClusterSS | Calculate within-cluster sum of squares |
