get_pathways {dce}R Documentation

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"))

[Package dce version 1.2.0 Index]