filter_scExp: Filter cells and features

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

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,
  percentMin = 1,
  bin_min_count = 2,
  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)
percentMin	Minimum percent of cells 'ON' in feature. (1)
bin_min_count	Minimum number of counts to define if cell is 'ON'. (2)
verbose	(TRUE)

Value

Returns a filtered SingleCellExperiment object.

Examples

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

# No feature filtering (all features are valuable)
scExp. = filter_scExp(scExp,percentMin=0)

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

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.