summarize_genes: Summarize the differential connectivity of genes over all...

In dnapath: Differential Network Analysis using Gene Pathways

Summarize the differential connectivity of genes over all pathways.

Description

Summarize the differential connectivity of genes over all pathways.

Usage

summarize_genes(x, alpha = 0.1, monotonized = FALSE)

Arguments

x	A 'dnapath_list' object from dnapath.
alpha	Threshold for p-values of gene DC scores. Used to determine the number of pathways that each gene is differentially connected in. 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 across all pathways.

See Also

summarize_pathways, 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_genes(results) # Summary of genes across all pathways.
summarize_genes(results[[1]]) # Summary of genes within the first pathway.

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