Reconstruction of Clones from Integration Site Readouts and Visualization

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Documentation for package ‘MultIS’ version 0.6.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

bushmanplot	Create a stacked area plot that represents the abundance of integration sites over time.
bw	Calculate the bw index
convert_columnwise_relative	Converts a matrix to relative abundances
evaluate_clustering	Evaluate a clustering using the given method
evaluate_clustering_bw	Evaluate a clustering using the bw index
evaluate_clustering_custom	Evaluate a clustering using a custom evaluation function
evaluate_clustering_dunn	Evaluate a clustering using the dunn index
evaluate_clustering_ptbiserial	Evaluate a clustering using the point-biserial index
evaluate_clustering_sdindex	Evaluate a clustering using the SD-index
evaluate_clustering_silhouette	Evaluate a clustering using the silhouette index
filter_at_tp_biggest_n	Filters a matrix of readouts for the n biggest IS at a certain measurement
filter_at_tp_min	Filters a matrix of readouts for IS that have a minimum occurrence in some measurement
filter_combine_measurements	Combines columns that have the same name. The columns are joined additively.
filter_is_names	Shortens the rownames of a readout matrix to the shortest distinct prefix
filter_match	Filters for columns containing a certain substring.
filter_measurement_names	Splits a vector of strings by a given regexp, selects and rearranges the parts and joins them again
filter_names	Filters a vector of names and returns the shortest common prefix.
filter_nr_tp_min	Filters for a minimum number of time points/measurements
filter_zero_columns	Removes columns that only contain 0 or NA.
filter_zero_rows	Removes rows that only contain 0 or NA.
find_best_nr_cluster	Finds the best number of clusters according to silhouette
get_similarity_matrix	Generate a similarity matrix
ggplot_colors	Get the default ggplot color palette or a color palette based on the ggplot palette, but with sub-colors that differ in their luminance
lineplot_split_clone	Show line plots of all integration sites over time, split into facets by their respective clone.
normalize_timecourse	Normalizes a time course using a given mapping from integration sites to clones.
plot.clusterObj	Plots the clustering based on a clustering object
plot.ISSimilarity	Plots the similarity of integration sites
plot.timeseries	Plots time series data, which consists of multiple measurements over time / place (cols) of different clones / integration sites (rows).
plot_rsquare	Plots R^2 of two integration sites
reconstruct	Apply a clustering algorithm to a given time course.
reconstruct_kmedoid	Calculate the k-medoids clustering for a given time course.
reconstruct_recursive	Apply a clustering algorithm recursively to a given time course.
weighted_spring_model	Plot the relationship of integration sites as a graph.