filter_scExp: Filter cells and features

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Filter cells and features

Description

Function to filter out cells & features from SingleCellExperiment based on total count per cell, number of cells 'ON' in features and top covered cells that might be doublets.

Usage

filter_scExp(
  scExp,
  min_cov_cell = 1600,
  quant_removal = 95,
  min_count_per_feature = 10,
  verbose = TRUE
)

Arguments

scExp	A SingleCellExperiment object.
min_cov_cell	Minimum counts for each cell. (1600)
quant_removal	Centile of cell counts above which cells are removed. (95)
min_count_per_feature	Minimum number of reads per feature (10).
verbose	(TRUE)

Value

Returns a filtered SingleCellExperiment object.

Examples

raw <- create_scDataset_raw()
scExp = create_scExp(raw$mat, raw$annot)
scExp. = filter_scExp(scExp)

# No feature filtering (all features are valuable)
scExp. = filter_scExp(scExp,min_count_per_feature=30)

# No cell filtering (all features are valuable)
scExp. = filter_scExp(scExp,min_cov_cell=0,quant_removal=100)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.