mapToReactome: map transcripts or genes to Reactome pathways, using a cache...

In arcolombo/TxDbLite: Lightweight SQLite-based annotation classes/packages for use with arkas

Description

map transcripts or genes to Reactome pathways, using a cache if possible

Usage

mapToReactome(IDs, type = c("transcript", "gene"),
  species = "Homo sapiens", build = 84, asNames = FALSE,
  asUrls = FALSE, useCache = TRUE)

Arguments

IDs	the identifiers to map
type	transcript- or gene-level mappings? (default: transcript)
species	what species are the IDs from? (default:Homo sapiens)
build	what build the IDs are from? (default:84)
asNames	boolean, convert the terms to full pathway names? (FALSE)
asUrls	boolean, convert terms to Reactome website URLs? (FALSE)
useCache	use the cache? (TRUE; do not change unless maintaining)

Value

a list of mappings for the supplied IDs

Examples

 mapToReactome("ENSG00000234258", type="gene")
           mapToReactome("ENST00000387459", asNames=TRUE)

arcolombo/TxDbLite documentation built on July 10, 2020, 12:27 a.m.