Function to annotate feature data in ExpressionSet, Seurat, or SingleCellExperiment objects

This function annotates feature data with scRNA data using biomaRt

scprep_biomart(
  dataset = dataset,
  ensembl_target = ensembl_target,
  reference = reference
)

Arguments

dataset

ExpressionSet, Seurat, or SingleCellExperiment object

ensembl_target

Species input for biomaRt feature annotation

reference

Reference genome (on annotation.csv & SampleSheet.csv): "refdata-cellranger-GRCh38-3.0.0" or "GRCh38_pre-mRNA" for Ensembl 93; "refdata-gex-GRCh38-2020-A" or "GRCh38_pre-mRNA-2020-A" for Ensembl 98

Value

Object of same type as input containing annotated feature data

Examples

if (FALSE) {
scprep_biomart(dataset=object, ensembl_target="hsapiens_gene_ensembl", 
               reference="refdata-cellranger-GRCh38-3.0.0")
}