summary.dnapath_list {dnapath}R Documentation

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.
[Package dnapath version 0.7.4 Index]