summary.dnapath_list: Summary function for 'dnapath_list' object.

In dnapath: Differential Network Analysis using Gene Pathways

Summary function for 'dnapath_list' object.

Description

Summary function for 'dnapath_list' object.

Usage

## S3 method for class 'dnapath_list'
summary(
  object,
  by_gene = FALSE,
  alpha_pathway = 1,
  alpha_gene = 0.1,
  monotonized = FALSE,
  ...
)

Arguments

object	A 'dnapath_list' object from dnapath.
by_gene	If TRUE, summarizes the differential network analysis by genes instead of by pathways.
alpha_pathway	Threshold for p-values of pathway DC scores; used to subset the results. 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. 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.
...	Additional arguments are ignored.

Value

Summarizes the differential network analysis results.

See Also

summarize_pathways, summarize_genes

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)
summary(results) # Summary across all pathways in the analysis.

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