summarize_genes_for_pathway

Summarize differential connectivity of genes in a pathway

internal

Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.

Tyler Grimes

dnapath

Differential Network Analysis using Gene Pathways

Somnath Datta

summarize_genes_for_pathway function

<dl><dt>x</dt>
<dd>A 'dnapath' object of a single pathway.</dd>
<dt>alpha</dt>
<dd>Threshold for p-values of gene DC scores, used to
subset the x. If NULL (or 1), x for all genes are shown.</dd>
<dt>monotonized</dt>
<dd>If TRUE, monotonized p-values are used.</dd></dl>

Arguments

Summarize differential connectivity of genes in a pathway — summarize_genes_for_pathway

<dl>

<dt>x</dt>
<dd>A 'dnapath' object of a single pathway.</dd>


<dt>alpha</dt>
<dd>Threshold for p-values of gene DC scores, used to
subset the x. If NULL (or 1), x for all genes are shown.</dd>


<dt>monotonized</dt>
<dd>If TRUE, monotonized p-values are used.</dd>

</dl>

summarize_genes_for_pathway: Summarize differential connectivity of genes in a pathway

Description

Usage

Value

Arguments