load_pathways: Loads the pathways object.

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

Loads the pathways object.

Description

Loads the pathways object, which includes information about the pathways to be analyzed.

Usage

load_pathways(species, pathways_list = NULL)

Arguments

species	Species of the samples.
pathways_list	Vector of the IDs of the pathways to load. By default all available pathways are load.

Details

The object of pathways includes information about the pathways and the subpathways which will be analyzed. This object must be provided to some of the functions (like hipathia or quantify_terms) in the package. These functions will analyze all the pathways included in this object. By default, all available pathways are load. In order to restrict the analysis to a predefined set of pathways, specify the set of pathways to load with the parameter pathways_list.

Value

An pathways object including * species Species to which the pathways are related. * pathigraphs List of Pathigraph objects. Each Pathigraph contains the necessary information of a pathway for it to be analyzed with Hipathia. * all_genes List of all the genes included in the selection of pathways stored in pathigraphs. * eff_norm Vector of normalization values for effector subpathways. * path_norm Vector of normalization values for decomposed subpathways.

Examples

## Not run: pathways <- load_pathways("hsa")   # Loads all pathways for human
pathways <- load_pathways("mmu", c("mmu03320", "mmu04024", "mmu05200"))
   # Loads pathways 03320, 04024 and 05200 for mouse

martahidalgo/hipathia documentation built on Jan. 12, 2023, 1:44 p.m.