dnapath (version 0.7.6)

summarize_edges: 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)

Value

A tibble summarizing the differential connections in the pathway.

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.

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]])