summarize_pathways: Summarize the differential connectivity of pathways.

In dnapath: Differential Network Analysis using Gene Pathways

Summarize the differential connectivity of pathways.

Description

Summarize the differential connectivity of pathways.

Usage

summarize_pathways(x, alpha = 1, alpha_gene = 0.1, monotonized = FALSE)

Arguments

x	A 'dnapath_list' object from dnapath.
alpha	Threshold for p-values of pathway DC scores. Defaults to 1, which leads to results for all pathways being 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. 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.

Value

A tibble summarizing the differential connectivity of genes in the pathway.

See Also

summarize_genes, summarize_edges

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_pathways(results)

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