make_gene_annotation: Create a 'dataframe' with annotation of SCE object's genes...

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

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

Description

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.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.