R: Summary function for 'dnapath' object.

summary.dnapath {dnapath} | R Documentation

## 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.

[Package dnapath version 0.7.4 Index]