Create a dataframe with annotation of SCE object's genes using an AnnotationDbi package.

The following columns are retrieved from the AnnotationDbi package: SYMBOL, GENENAME, ENTREZID. Multi-mapping entities are collapsed by "," (i.e. a single ENSEMBL ID having multiple symbols, etc.). Unknown symbols are replaced by the corresponding ENSEMBL IDs.

Usage

make_gene_annotation(sce, annotation_db_file)

Arguments

sce

A SingleCellExperiment object.

annotation_db_file

A character scalar: path to SQLite file of annotation DB, e.g. org.Hs.eg.db$conn@dbname.

Value

A dataframe with annotation.