CMIBiCondimat2mat

Computes the normalized conditional mutual information (CMI) between corresponding rows of two matrices,
given two condition variables, normalized by their individual information content. CMI is calculated using the specified number of bins and spline order.

The biases introduced in association measures, particularly mutual information,
are influenced by factors such as tumor purity, mutation burden, and hypermethylation.
This package provides the estimation of conditional mutual information (CMI) and its
statistical significance with a focus on its application to multi-omics data. Utilizing
B-spline functions (inspired by Daub et al. (2004) <doi:10.1186/1471-2105-5-118>), the package offers tools to estimate the association between heterogeneous multi-
omics data, while removing the effects of confounding factors. This helps to unravel complex
biological interactions. In addition, it includes methods to evaluate the statistical significance
of these associations, providing a robust framework for multi-omics data integration and
analysis. This package is ideal for researchers in computational biology, bioinformatics,
and systems biology seeking a comprehensive tool for understanding interdependencies in
omics data.

Gaojianyong Wang

conMItion

Conditional Mutual Information Estimation for Multi-Omics Data

CMIBiCondimat2mat function

<dl><dt>mat1</dt>
<dd>A numeric matrix. For example, each row represents a gene and each column represents a sample.</dd>
<dt>mat2</dt>
<dd>Another numeric matrix to compare against. Must have the same dimensions as `mat1`.</dd>
<dt>condi1</dt>
<dd>A numeric condition vector, matching the number of columns in `mat1`.</dd>
<dt>condi2</dt>
<dd>Another numeric condition vector, matching the number of columns in `mat1`.</dd>
<dt>bin</dt>
<dd>An integer specifying the number of bins. Default is 6.</dd>
<dt>sp_order</dt>
<dd>An integer specifying the spline order. Must be less than `bin`. Default is 2.</dd></dl>

Arguments

Normalized Conditional Mutual Information Between Two Matrices Given Two Conditions — CMIBiCondimat2mat

<dl>

<dt>mat1</dt>
<dd>A numeric matrix. For example, each row represents a gene and each column represents a sample.</dd>


<dt>mat2</dt>
<dd>Another numeric matrix to compare against. Must have the same dimensions as `mat1`.</dd>


<dt>condi1</dt>
<dd>A numeric condition vector, matching the number of columns in `mat1`.</dd>


<dt>condi2</dt>
<dd>Another numeric condition vector, matching the number of columns in `mat1`.</dd>


<dt>bin</dt>
<dd>An integer specifying the number of bins. Default is 6.</dd>


<dt>sp_order</dt>
<dd>An integer specifying the spline order. Must be less than `bin`. Default is 2.</dd>

</dl>

CMIBiCondimat2mat: Normalized Conditional Mutual Information Between Two Matrices Given Two Conditions

Description

Usage

Value

Arguments

Examples