Man pages for MultIS
Reconstruction of Clones from Integration Site Readouts and Visualization

bushmanplotCreate a stacked area plot that represents the abundance of...
bwCalculate the bw index
convert_columnwise_relativeConverts a matrix to relative abundances
evaluate_clusteringEvaluate a clustering using the given method
evaluate_clustering_bwEvaluate a clustering using the bw index
evaluate_clustering_customEvaluate a clustering using a custom evaluation function
evaluate_clustering_dunnEvaluate a clustering using the dunn index
evaluate_clustering_ptbiserialEvaluate a clustering using the point-biserial index
evaluate_clustering_sdindexEvaluate a clustering using the SD-index
evaluate_clustering_silhouetteEvaluate a clustering using the silhouette index
filter_at_tp_biggest_nFilters a matrix of readouts for the n biggest IS at a...
filter_at_tp_minFilters a matrix of readouts for IS that have a minimum...
filter_combine_measurementsCombines columns that have the same name. The columns are...
filter_is_namesShortens the rownames of a readout matrix to the shortest...
filter_matchFilters for columns containing a certain substring.
filter_measurement_namesSplits a vector of strings by a given regexp, selects and...
filter_namesFilters a vector of names and returns the shortest common...
filter_nr_tp_minFilters for a minimum number of time points/measurements
filter_zero_columnsRemoves columns that only contain 0 or NA.
filter_zero_rowsRemoves rows that only contain 0 or NA.
find_best_nr_clusterFinds the best number of clusters according to silhouette
get_similarity_matrixGenerate a similarity matrix
ggplot_colorsGet the default ggplot color palette or a color palette based...
lineplot_split_cloneShow line plots of all integration sites over time, split...
normalize_timecourseNormalizes a time course using a given mapping from...
plot.clusterObjPlots the clustering based on a clustering object
plot.ISSimilarityPlots the similarity of integration sites
plot_rsquarePlots R^2 of two integration sites
plot.timeseriesPlots time series data, which consists of multiple...
reconstructApply a clustering algorithm to a given time course.
reconstruct_kmedoidCalculate the k-medoids clustering for a given time course.
reconstruct_recursiveApply a clustering algorithm recursively to a given time...
weighted_spring_modelPlot the relationship of integration sites as a graph.
MultIS documentation built on Aug. 6, 2021, 5:07 p.m.