R: Summarize differential connections for a pathway

summarize_edges {dnapath} | R Documentation

## Summarize differential connections for a pathway

### Description

Summarize differential connections for a pathway

### Usage

    summarize_edges(x, alpha = 0.1, monotonized = FALSE, require_dc_genes = FALSE)

### Arguments

`x` | A 'dnapath' object from `dnapath`.
`alpha` | Threshold for p-values of edge DC scores. 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.
`require_dc_genes` | If TRUE, the gene-level differential connectivity p-value of the two genes for a given edge are also considered when deciding whether an edge is differentially connected. If neither gene is significantly differentially connected, then the edge between them will not be either.

### Value

A tibble summarizing the differential connections in the pathway.

### 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)
    summarize_edges(results[[1]])

[Package dnapath version 0.7.4 Index]