load_pathways {hipathia} | R Documentation

## 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

[Package hipathia version 2.2.1 Index]