get_reactome_pathways | R Documentation |
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
.
get_reactome_pathways( species, overlap_limit = 0.9, min_size = 10, max_size = 50, verbose = TRUE )
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 |
max_size |
The maximum pathway size. Any Reactome pathways with more
than |
verbose |
Set to FALSE to turn off messages. |
A named list of vectors. Each vector corresponds to a Reactome pathway and contains the entrezgene IDs of the genes in that pathway.
reactomednapath
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.
# 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)
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