annotate_integrated_sce: Annotate integrated, reduced dimension, and clustered...

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Annotate integrated, reduced dimension, and clustered SingleCellExperiment object

Description

Annotate integrated, reduced dimension, and clustered SingleCellExperiment object

Usage

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()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.