R: Remove pathways with non-significant DC scores.

filter_pathways {dnapath} | R Documentation

## Remove pathways with non-significant DC scores.

### Description

Remove pathways with non-significant DC scores.

### Usage

    filter_pathways(x, alpha_pathway = NULL, monotonized = FALSE)

### Arguments

`x` | A 'dnapath_list' object from `dnapath`.
`alpha_pathway` | Threshold for pathway p-values to determine significance. If NULL, defaults to 0.05 or the minimum possible threshold (based on the number of permutatiosn that were run).
`monotonized` | If TRUE, monotonized p-values are used.

### Value

A 'dnapath_list' object containing only those pathways with differential connectivity p-values below `alpha`.

### 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)
    results_sig <- filter_pathways(results)

[Package dnapath version 0.7.4 Index]