R: Summary function for 'dnapath_list' object.

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]