R: Summarize the differential connectivity of pathways.

summarize_pathways {dnapath} | R Documentation

## Summarize the differential connectivity of pathways.

### Description

Summarize the differential connectivity of pathways.

### Usage

    summarize_pathways(x, alpha = 1, alpha_gene = 0.1, monotonized = FALSE)

### Arguments

`x` | A 'dnapath_list' object from `dnapath`.
`alpha` | Threshold for p-values of pathway DC scores. Defaults to 1, which leads to results for all pathways being 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.

### Value

A tibble summarizing the differential connectivity of genes in the pathway.

### 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)
    summarize_pathways(results)

[Package dnapath version 0.7.4 Index]