summarize_edges: Summarize differential connections for a pathway

In dnapath: Differential Network Analysis using Gene Pathways

Summarize differential connections for a pathway

Description

Summarize differential connections for a pathway

Usage

summarize_edges(x, alpha = 0.1, monotonized = FALSE, require_dc_genes = FALSE)

Arguments

x	A 'dnapath' object from dnapath.
alpha	Threshold for p-values of edge DC scores. Defaults to 0.1 or the minimum possible threshold for the number of permutations performed, whichever is greater.
monotonized	If TRUE, monotonized p-values are used.
require_dc_genes	If TRUE, the gene-level differential connectivity p-value of the two genes for a given edge are also considered when deciding whether an edge is differentially connected. If neither gene is significantly differentially connected, then the edge between them will not be either.

Value

A tibble summarizing the differential connections in the pathway.

See Also

summarize_pathways, summarize_genes

Examples

data(meso)
data(p53_pathways)
set.seed(0)
results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways,
                   group_labels = meso$groups, n_perm = 10)
summarize_edges(results[[1]])

dnapath documentation built on May 9, 2022, 9:05 a.m.