Bin and/or Cell-wise quality filtering — filter

Note – this filters GC bins, then bins by counts, and then cells. So the denominator changes at each step.

Usage

filter_sce(
  sce,
  assay_name = "counts",
  which = c("bins", "cells"),
  min_bin_counts = 1,
  min_bin_prop = 0.95,
  min_cell_counts = min_bin_counts,
  min_cell_prop = min_bin_prop,
  flag_only = FALSE,
  gc_range = c(-Inf, Inf)
)

Arguments

sce: SingleCellExperiment object
assay_name: Name of assay to pull counts from. Ideally raw counts
which: Filter cells or bins
min_bin_counts: A bin requires at least min_bin_counts across min_bin_prop proportion of cells to be kept
min_bin_prop: Minimum proportion of cells with at least min_bin_counts per bin in order to keep a bin
min_cell_counts: A cell requires at least min_cell_counts across min_cell_prop proportion of bins to be kept
min_cell_prop: Minimum proportion of bins with at least min_cell_counts per cell in order to keep a cell
flag_only: Only flag cells/bins, do not remove
gc_range: GC range for bins to keep. Removes large GC outliers

Value

SingleCellExperiment object