annotate_celltype_metrics: Annotate a SingleCellExperiment With Cell-type Metrics

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

Annotate a SingleCellExperiment With Cell-type Metrics

Description

Annotate a SingleCellExperiment With Cell-type Metrics

Usage

annotate_celltype_metrics(
  sce,
  cluster_var = "clusters",
  celltype_var = "cluster_celltype",
  unique_id_var = "manifest",
  facet_vars = c("manifest", "group", "sex"),
  input_reduced_dim = "UMAP_Liger",
  metric_vars = c("pc_mito", "pc_ribo", "total_counts", "total_features_by_counts"),
  ...
)

Arguments

sce	a SingleCellExperiment object
cluster_var	the colData variable with the cluster numbers
celltype_var	the colData variable with the celltype alias
unique_id_var	the colData variable with the unique sample name
facet_vars	the colData variable(s) for grouped analyses
input_reduced_dim	the reducedDim slot used for clustering
metric_vars	the numeric colData variable(s) for metric comparisons
...	additional parameters

Value

sce a annotated SingleCellExperiment object

See Also

Other annotation functions: .preprocess_seurat_object(), annotate_integrated_sce(), 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.