i.inp: i.inp Information Index (I index) for 2-Way, 2 Column Table

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

Description

The I-index is a measure of overlap in two way tables based on the generalized mutual information statistic. This function implements a special case of table with two columns only. In general, the I-index measures dependence in any 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).

Usage

i.inp(x, alpha = 1, CI = 0.95, resample = 100, graph = FALSE, 
csv_output = FALSE, PlugIn = FALSE, size = 1, CVG = FALSE, 
saveBootstrap = FALSE)

Arguments

x	a matrix containing input populations
alpha	I index of order alpha < 1 puts more weight on the rare species and the I Index of order alpha > 1 puts more weight on the abundant ones, default = 1
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
graph	default = FALSE, plot the results of hierarchical clustering of pairwise analysis of I 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 <- i.inp(x, resample = 25)

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