dnapath (version 0.6.4)

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

Description

Summarize the differential connectivity of genes over all pathways.

Usage

summarize_genes(x, alpha_gene = NULL, monotonized = FALSE)

Arguments

x

A 'dnapath_list' object from dnapath.

alpha_gene

Threshold for p-values of gene DC scores. Used to determine the number of pathways that each gene is differentially connected in. If NULL, defaults to 0.05 or the minimum possible threshold (based on the number of permutatiosn that were run).

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

# NOT RUN {
data(meso)
data(p53_pathways)
set.seed(0)
results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways,
                   groups = meso$groups, n_perm = 10)
summarize_genes(results) # Summary of genes across all pathways.
summarize_genes(results[[1]]) # Summary of genes within the first pathway.
# }