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 |
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]