convert_gene_identifier: Title

In Close-your-eyes/scexpr: Lots of helpers and wrappers to analyze scRNAseq data sets

Title

Description

Convert gene identifiers from ident_in to ident_out with AnnotationDbi while taking care of known duplicates and providing aliases. For human org.Hs.eg.db is used, for mouse org.Mm.eg.db.

Usage

convert_gene_identifier(
  idents,
  ident_in = "SYMBOL",
  ident_out = c("ENTREZID", "ALIAS", "GENENAME"),
  species = c("Hs", "Mm"),
  return = c("data.frame", "vector")
)

Arguments

idents	character vector of gene indentifiers
ident_in	type of identifier provided in idents
ident_out	type(s) of identifier(s) to return
return

Details

keytypes(org.Hs.eg.db) or colums(org.Hs.eg.db) are: ACCNUM ALIAS ENSEMBL ENSEMBLPROT ENSEMBLTRANS ENTREZID ENZYME EVIDENCE EVIDENCEALL GENENAME GENETYPE GO GOALL IPI MAP OMIM ONTOLOGY ONTOLOGYALL PATH PFAM PMID PROSITE REFSEQ SYMBOL UCSCKG UNIPROT

Close-your-eyes/scexpr documentation built on April 21, 2023, 10:27 a.m.