get_reactome_pathways: Obtain Reactome pathways

In dnapath: Differential Network Analysis using Gene Pathways

Obtain Reactome pathways

Description

Connects to reactome.db \insertCitereactomednapath 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

\insertRef

reactomednapath

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)

dnapath documentation built on May 9, 2022, 9:05 a.m.