filter_sce: Filter SingleCellExperiment according to QC metrics Quality...

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

Filter SingleCellExperiment according to QC metrics Quality control metrics previously calculated are used to subset the SingleCellExperiment for both cells and genes passing QC criteria previously specified in the annotate_sce_genes and annotate_sce_cells functions

Description

Filter SingleCellExperiment according to QC metrics Quality control metrics previously calculated are used to subset the SingleCellExperiment for both cells and genes passing QC criteria previously specified in the annotate_sce_genes and annotate_sce_cells functions

Usage

filter_sce(sce, filter_genes = TRUE, filter_cells = TRUE)

Arguments

sce	a SingleCellExperiment object
filter_genes	if set FALSE, genes will not be filtered
filter_cells	if set FALSE, cells will not be filtered

Value

sce a SingleCellExperiment object filtered for QC passed cells and genes, with QC metrics annotations removed

See Also

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