| summarize_genes {dnapath} | R Documentation |
Summarize the differential connectivity of genes over all pathways.
summarize_genes(x, alpha = 0.1, monotonized = FALSE)
x |
A 'dnapath_list' object from |
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. |
A tibble summarizing the differential connectivity of genes across all pathways.
summarize_pathways, summarize_edges
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.