The I-index is a measure of overlap in two way tables based on the generalized mutual information statistic. The I-index measures dependence among columns of two-way tables, taking values between 0 and 1. It returns a value of zero when the table columns form an orthogonal system and a value of one when the table columns rank is one. The value of the parameter alpha is related to the structure of dependence, as described in Rempala and Seweryn (2013).
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x |
a matrix containing input populations |
alpha |
I index of order alpha, must be between 0 and 1, default = 0.5 |
CVG |
I index of order alpha = coverage. If CVG = TRUE argument alpha is ignored; default = FALSE |
CI |
Confidence Interval default = 0.95, range (0, 1) |
resample |
set number of repetitions, default = 100 |
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 |
Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak pietrzak.20@osu.edu
Rempala G.A., Seweryn M. (2013) Methods for diversity and overlap analysis in T-cell receptor populations. J Math Biol 67:1339-68
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