get_pathways_summary {hipathia} | R Documentation

## Compute pathway summary

### Description

Computes a summary of the results, summarizing the number and proportion of up- and down-regulated subpathways in each pathway.

### Usage

    get_pathways_summary(comp, metaginfo, conf = 0.05)

### Arguments

`comp` | Comparison data frame as returned by the `do_wilcoxon` function.
`metaginfo` | Pathways object
`conf` | Level of significance of the comparison for the adjusted p-value. Default is 0.05.

### Value

Table with the summarized information for each of the pathways. Rows are the analized pathways. Columns are: * `num_total_paths` Number of total subpathways in which each pathway is decomposed. * `num_significant_paths` Number of significant subpathways in the provided comparison. * `percent_significant_paths` Percentage of significant subpathways from the total number of subpathways in a pathway. * `num_up_paths` Number of significant up-regulated subpathways in the provided comparison. * `percent_up_paths` Percentage of significant up-regulated subpathways from the total number of subpathways in a pathway. * `num_down_paths` Number of significant down-regulated subpathways in the provided comparison. * `percent_down_paths` Percentage of significant down-regulated subpathways from the total number of subpathways in a pathway.

### Examples

    data(comp)
    pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
    "hsa04012"))
    get_pathways_summary(comp, pathways)

[Package hipathia version 1.0.0 Index]