Annotate integrated, reduced dimension, and clustered SingleCellExperiment object

Annotate integrated, reduced dimension, and clustered SingleCellExperiment object

annotate_integrated_sce(
  sce,
  categorical_covariates = list(),
  input_reduced_dim = "tSNE"
)

Arguments

sce

SingleCellExperiment object

categorical_covariates

list of categorical variables

input_reduced_dim

which reduced dim to use for integration and clustering. Either "tSNE" or "UMAP" (default "tSNE").

Value

sce annotated SingleCellExperiment object

See also

Other annotation functions: .preprocess_seurat_object(), annotate_celltype_metrics(), annotate_merged_sce(), annotate_sce(), annotate_sce_cells(), annotate_sce_genes(), filter_sce(), find_cells(), find_singlets(), generate_sce(), map_ensembl_gene_id(), merge_sce(), read_metadata(), report_celltype_metrics(), report_celltype_model(), report_merged_sce(), report_qc_sce(), run_doubletfinder(), sce_to_seu()