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.
gene2symbol(x, ensdb, dups = c("omit", "pass"))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.
Either a vector of ensembl gene ids to convert or a 'cellMarkers' class object.
An ensembl database object loaded via the AnnotationHub
bioconductor package.
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.
cellMarkers()