getAnnotationPathways: Returns list of annotations for given Entrez gene IDs

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Returns list of annotations for given Entrez gene IDs

Description

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

Usage

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).

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.