Given an annotation object, this function will overlap genes with bins and place the results in the metadata slot gene_overlaps. This function will also attempt to annotate cancer genes using OncoKB.
Usage
overlap_genes(sce, ensDb, gene_biotype = "all")
Arguments
- sce
SingleCellExperiment object
- ensDb
EnsemblDb object such as EnsDb.Hsapiens.v86::EnsDb.Hsapiens.v86
- gene_biotype
Gene biotypes to overlap. Defaults to "all". Use "protein_coding" to keep only protein coding genes
Value
SingleCellExperiment object with gene overlaps in sce@metadata$gene_overlaps