get_pathways_summary: Compute pathway summary

In babelomics/hipathia: HiPathia: High-throughput Pathway Analysis

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)

babelomics/hipathia documentation built on July 27, 2022, 2:23 p.m.