filter_pathways: Remove pathways with non-significant DC scores.

In dnapath: Differential Network Analysis using Gene Pathways

Remove pathways with non-significant DC scores.

Description

Remove pathways with non-significant DC scores.

Usage

filter_pathways(x, alpha_pathway = NULL, monotonized = FALSE)

Arguments

x	A 'dnapath_list' object from dnapath.
alpha_pathway	Threshold for pathway p-values to determine significance. 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 'dnapath_list' object containing only those pathways with differential connectivity p-values below alpha.

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)
results_sig <- filter_pathways(results)

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