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

In dnapath: Differential Network Analysis using Gene Pathways

Summary function for 'dnapath' object.

Description

Summary function for 'dnapath' object.

Usage

## S3 method for class 'dnapath'
summary(object, by_gene = TRUE, alpha = 1, monotonized = FALSE, ...)

Arguments

object	A 'dnapath' object from dnapath.
by_gene	If TRUE, summarizes the differential network analysis by genes; otherwise, summarizes by gene-gene interactions.
alpha	Threshold for p-values to determine significance; defaults to 1 and returns all results. If 'by_gene' is FALSE, then 'alpha' is used to filter edges. If 'by_gene' is TRUE, then 'alpha' is used to filter genes.
monotonized	If TRUE, monotonized p-values are used.
...	Additional arguments are ignored.

Value

Summarizes the differential network analysis result.

See Also

summarize_genes, summarize_edges

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[[1]]) # Summary of the first pathway in the results.

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