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

In RamsinghLab/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)

RamsinghLab/TxDbLite documentation built on March 14, 2021, 10:49 a.m.