gene2symbol: Converts ensembl gene ids to symbols

In cellGeometry: Geometric Single Cell Deconvolution

Converts ensembl gene ids to symbols

Description

Uses a loaded ensembl database to convert ensembl gene ids to symbol. If a vector is provided, a vector of symbols is returned. If a cellMarkers object is provided, the rownames in the genemeans, genemeans_filtered, groupmeans and groupmeans_filtered elements are changed to symbol and the cellMarkers object is returned.

Usage

gene2symbol(x, ensdb, dups = c("omit", "pass"))

Arguments

x	Either a vector of ensembl gene ids to convert or a 'cellMarkers' class object.
ensdb	An ensembl database object loaded via the AnnotationHub bioconductor package.
dups	Character vector specifying action for duplicated gene symbols. "omit" means that duplicated gene symbols are not replaced, but left as ensembl gene ids. "pass" means that all gene ids are replaced where possible even if that leads to duplicates. Duplicates can cause problems with rownames and updateMarkers() in particular.

Value

If x is a vector, a vector of symbols is returned. If no symbol is available for particular ensembl id, the id is left untouched. If x is a 'cellMarkers' class object, a 'cellMarkers' object is returned with rownames in the results elements and genesets converted to gene symbols, and an extra element symbol containing a named vector of converted genes.

See Also

cellMarkers()

cellGeometry documentation built on April 20, 2026, 1:06 a.m.