summary.dnapath_list: Summary function for 'dnapath_list' object.

In tgrimes/dnapath2: Differential Network Analysis Using Gene Pathways

Description

Summary function for 'dnapath_list' object.

Usage

## S3 method for class 'dnapath_list'
summary(x, by_gene = FALSE,
  alpha_pathway = NULL, alpha_gene = NULL, ...)

Arguments

x	A 'dnapath_list' object.
by_gene	If TRUE, summarizes the differential network analysis by genes instead of by pathways.
alpha_pathway	Threshold for p-values of pathway DC scores; used to subset the results. If NULL (or 1), results for all pathways are shown.
alpha_gene	Threshold for p-values of gene DC scores. Used to determine the number of genes that are differentially connected within each pathway. If NULL, defaults to 0.05 or the minimum possible threshold (based on the number of permutatiosn that were run).
...	Additional arguments are ignored.

Value

Summarizes the differential network analysis results.

tgrimes/dnapath2 documentation built on May 21, 2020, 5:53 p.m.