Returns list of annotations for given Entrez gene IDs

Returns list of Reactome or GO annotations for given Entrez gene IDs

getAnnotationPathways(
  query.genes,
  db = c("Bader"),
  ontology = c("BP"),
  species = c("Hs"),
  msigdb.collection = "H",
  msigdb.subcollection = NULL
)

Arguments

query.genes

Entrez IDs of query genes

db

Database to retrieve annotations from. One of:

  • "Bader" - Default. List of pathway annotations curated by Bader lab (http://baderlab.org/GeneSets)

  • "Reactome"

  • "GO" - Requires additional specification of ontology.

  • "KEGG"

  • "msigdb" - Requires additional specification of msigdb.collection, and optionally msigdb.subcollection.

ontology

GO ontologies to retrieve if GO db is selected. One of:

  • "BP" - Default. Biological processes

  • "MF" - Molecular functions

  • "CC" - Cellular components

species

"Mm" or "Hs". Default is "Hs".

msigdb.collection

Geneset collection (only if msigdb database used). See msigdbr() for additional details. One of:

  • "H" - Hallmark (Default)

  • "C1" - positional genesets

  • "C2" - curated genesets (CGP, CP)

  • "C3" - regulatory target genesets (MIR, TFT)

  • "C4" - computational genesets (CGN, CM)

  • "C5" - ontology genesets (GO, GO:BP, GO:CC, GO:MF, HPO)

  • "C6" - oncogenic signature genesets

  • "C7" - immunologic signatures

  • "C8" - cell type signature genesets

msigdb.subcollection

Subcollection corresponding to specified msigdb collection. Possible subcollections for each collection are indicated in parantheses above.

Value

Named list of vectors with gene sets (Entrez format).