get_reactome_pathways {dnapath}

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)