get_pathways: Easy pathway network access

In kpj/dce: Pathway Enrichment Based on Differential Causal Effects

Easy pathway network access

Description

Easy pathway network access

Usage

get_pathways(
  query_species = "hsapiens",
  database_list = NULL,
  remove_empty_pathways = TRUE,
  pathway_list = NULL
)

Arguments

query_species	For which species
database_list	Which databases to query. Query all if 'NULL'.
remove_empty_pathways	Discard pathways without nodes
pathway_list	List mapping database name to vector of pathway names to download

Value

list of pathways

Examples

pathways <- get_pathways(
  pathway_list = list(kegg = c(
    "Protein processing in endoplasmic reticulum"
  ))
)
plot_network(as(pathways[[1]]$graph, "matrix"))

kpj/dce documentation built on Oct. 29, 2022, 1:40 a.m.