R: Summarize the differential connectivity of genes over all...

summarize_genes {dnapath} | R Documentation

## Summarize the differential connectivity of genes over all pathways.

### Description

Summarize the differential connectivity of genes over all pathways.

### Usage

    summarize_genes(x, alpha = 0.1, monotonized = FALSE)

### Arguments

`x` | A 'dnapath_list' object from `dnapath`.
`alpha` | Threshold for p-values of gene DC scores. Used to determine the number of pathways that each gene is differentially connected in. 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 across all pathways.

### See Also

`summarize_pathways`, `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_genes(results) # Summary of genes across all pathways.
    summarize_genes(results[[1]]) # Summary of genes within the first pathway.

[Package dnapath version 0.7.4 Index]