annotate_sce_cells: Add basic cell-wise annotations for a SingleCellExperiment

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

Add basic cell-wise annotations for a SingleCellExperiment

Description

Calculates the following QC metrics:

• qc_metric_total_counts - was the ensembl_gene_id found in biomaRt

• qc_metric_total_features_by_counts - is the gene mitochondrial

Usage

annotate_sce_cells(sce, ...)

Arguments

sce

a SingleCellExperiment object

...

See annotate_sce min_library_size the minimum number of counts per cell min_features the minimum number of features per cell (i.e. the minimum number of genes with >0 counts) max_mito the maximum proportion of counts mapping to mitochondrial genes (0 - 1) min_ribo max_ribo the maximum proportion of counts mapping to ribosomal genes (0 - 1) min_counts the minimum number of counts per cell in min_cells min_cells the minimum number of cells with min_counts

Value

sce a SingleCellExperiment object annotated with cell QC metrics

See Also

Other annotation functions: .preprocess_seurat_object(), annotate_celltype_metrics(), annotate_integrated_sce(), annotate_merged_sce(), annotate_sce(), 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.