GetGOTerms: Retrieve Gene Ontology (GO) Terms and Associated Genes

In jn-goe/gruffi: Gruffi identifies and removes stressed cells from brain organoid single-cell datasets.

Retrieve Gene Ontology (GO) Terms and Associated Genes

Description

Fetches genes associated with a specified Gene Ontology (GO) term and optionally opens the GO term page. The genes are retrieved using either the Ensembl database via biomaRt or from precomputed GO_genes results stored in the Seurat object.

Usage

GetGOTerms(
  obj = combined.obj,
  GO = "GO:0034976",
  assay = "RNA",
  data.base.access = c("biomaRt", "AnnotationDbi")[1],
  version = NULL,
  GRCh = NULL,
  genes.shown = 10,
  web.open = FALSE,
  overwrite.misc.GO_genes = FALSE,
  mirror = NULL
)

Arguments

obj	A Seurat object potentially containing precomputed GO_genes results. Default: combined.obj
GO	The GO term identifier for which to fetch associated genes. Default: 'GO:0034976'
assay	Assay to consider when retrieving precomputed GO_genes results.
data.base.access	Which tool to use to access gene list databases? Options: biomaRt (deault) or AnnotationDbi.
version	Ensembl version, useful if wanting to connect to an archived Ensembl version.
GRCh	GRCh version if not using the current GRCh38, currently this can only be 37 (via useEnsembl())
genes.shown	Number of genes shown, Default: 10
web.open	Logical; if TRUE, opens the web page for the specified GO term.
overwrite.misc.GO_genes	Overwrite preexisting gene set in misc$gruffi$GO[[make.names(GO)]].
mirror	Ensembl mirror to use, helpful if the default connection fails with default settings, mirror can be specified. Default: 'NULL'

Value

The input Seurat object with the retrieved genes associated with the specified GO term stored in obj@misc$gruffi$GO.

See Also

useEnsembl, getBM AnnotationDb-objects org.Hs.eg.db kollapse

jn-goe/gruffi documentation built on Nov. 7, 2024, 10:38 p.m.