li: li Sorensen Index

In divo: Tools for Analysis of Diversity and Similarity in Biological Systems

Description

The Sorensen similarity (overlap) index measures the overlap between two populations by taking the ratio of the number of species shared between the two populations, relative to the number of species in both populations. The index varies between zero (no overlap) and one (perfect overlap). It is closely related to the Jaccard index of similarity (implemented in function ji).

Usage

li(x, CI = 0.95, resample = 100, graph = FALSE, csv_output = FALSE, 
PlugIn = FALSE, size = 1, saveBootstrap = FALSE)

Arguments

x	a matrix containing input populations
CI	Confidence Interval default = 0.95, range (0, 1)
resample	set number of repetitions, default = 100
graph	default = FALSE, plot the results of hierarchical clustering of pairwise analysis of Sorensen Index; graph = 'fileName' user-defined output file name
csv_output	save the result of the analysis as .CSV file, default = FALSE; csv_output = 'fileName' user-defined output file name
PlugIn	standard plug-in estimator, default = FALSE
size	resampled fraction of the population, default = 1 (actual size of populations). The value should not be smaller than 10% of population (size = 0.1)
saveBootstrap	Saves bootstrap result to a file. Use saveBootstrap = TRUE to save bootstrap results to a Bootstrap folder in current directory; saveBootstrap = 'FolderName' - saves bootstrap results to user-named folder

Author(s)

Christoph Sadee, Maciej Pietrzak, Michal Seweryn, Cankun Wang, Grzegorz Rempala
Maintainer: Maciej Pietrzak [e-mail]

References

Rempala G.A., Seweryn M. (2013) Methods for diversity and overlap analysis in T-cell receptor populations. J Math Biol 67:1339-68

Examples

data(TCR.Data)
result <- li(x, resample = 50) 

divo documentation built on Dec. 18, 2019, 1:51 a.m.