R: Obtain Reactome pathways

get_reactome_pathways {dnapath} | R Documentation

## Obtain Reactome pathways

### Description

Connects to `reactome.db` (Ligtenberg 2019) to obtain a list of pathways for a given species. The pathway list is processed by combining any two pathways that have substantial overlap (default is over 90% overlap). This output if this function can be used for the `pathway_list` argument in `dnapath`.

### Usage

    get_reactome_pathways(
      species,
      overlap_limit = 0.9,
      min_size = 10,
      max_size = 50,
      verbose = TRUE
    )

### Arguments

`species` | A string, for example "Homo sapiens" or "Mus musculus", indicating the species to use.
`overlap_limit` | (Optional) Any pathways that have an overlap greater than overlap_limit are combined. Set to NULL to disable this option.
`min_size` | The minimum pathway size. Any Reactome pathways with fewer than `min_size` genes are removed from the list. Defaults to 10.
`max_size` | The maximum pathway size. Any Reactome pathways with more than `max_size` genes are removed from the list. Defaults to 50.
`verbose` | Set to FALSE to turn off messages.

### Value

A named list of vectors. Each vector corresponds to a Reactome pathway and contains the entrezgene IDs of the genes in that pathway.

### References

Ligtenberg W (2019). reactome.db: A Set of Annotation Maps for Reactome. R package version 1.68.0.

### See Also

The genes in the Reactome pathways use entrezgene IDs. These can be converted to gene symbols, if desired, using the `entrez_to_symbol` and `rename_genes` functions.

### Examples

    # Obtaining a pathway list for human (Homo sapiens).
    # In this example, overlapping pathways are not combined (this is
    # specified by setting overlap_limit to NULL).
    pathway_list <- get_reactome_pathways("Homo sapiens", overlap_limit = NULL,
                                          min_size = 10, max_size = 20)

[Package dnapath version 0.7.4 Index]