filter_cells_and_genes: Filter out cells and genes

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

Filter out cells and genes

Description

Filter out cells and genes

Usage

filter_cells_and_genes(
  object,
  min_UMIs = 1000,
  max_UMIs = 30000,
  min_detected_genes = 1000,
  max_detected_genes = 8000,
  min_percent_mito = 0,
  max_percent_mito = 10,
  genes_with_expressing_cells = 10,
  isRemovedDoublets = TRUE
)

Arguments

object	The SingCellaR object.
min_UMIs	The minimum UMI cutoff.
max_UMIs	The maximum UMI cutoff.
min_detected_genes	The minimum number of genes detected per cell.
max_detected_genes	The maximum number of genes detected per cell.
min_percent_mito	The minimum percent of UMIs from the mitocondrial genes.
max_percent_mito	The maximum percent of UMIs from the mitocondrial genes.
genes_with_expressing_cells	The cutoff for genes expressing in at least a number of cells.
isRemovedDoublets	remove doublets or not, default = TRUE. This requires doublet detection result from the function 'DoubletDetection_with_scrublet'

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.