summarize_pathways: Summarize the differential connectivity of pathways.

Description Usage Arguments Value See Also Examples

View source: R/summary.R

Description

Summarize the differential connectivity of pathways.

Usage

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summarize_pathways(x, alpha = NULL, alpha_gene = NULL, monotonized = FALSE)

Arguments

x

A 'dnapath_list' object from dnapath.

alpha

Threshold for p-values of pathway DC scores. If NULL (or 1), results for all pathways are 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. 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 in the pathway.

See Also

summarize_genes, summarize_edges

Examples

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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_pathways(results)

dnapath documentation built on Dec. 11, 2021, 9:54 a.m.