sc_atac_filter_cell_calling: filter cell calling

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

filter cell calling

Description

specify various qc cutoffs to select the desired cells

Usage

sc_atac_filter_cell_calling(
  mtx,
  cell_qc_metrics_file,
  min_uniq_frags = 0,
  max_uniq_frags = 50000,
  min_frac_peak = 0.05,
  min_frac_tss = 0,
  min_frac_enhancer = 0,
  min_frac_promoter = 0,
  max_frac_mito = 0.2
)

Arguments

mtx	The input matrix
cell_qc_metrics_file	A file containing qc statistics for each cell
min_uniq_frags	The minimum number of required unique fragments required for a cell
max_uniq_frags	The maximum number of required unique fragments required for a cell
min_frac_peak	The minimum proportion of fragments in a cell to overlap with a peak
min_frac_tss	The minimum proportion of fragments in a cell to overlap with a tss
min_frac_enhancer	The minimum proportion of fragments in a cell to overlap with a enhancer sequence
min_frac_promoter	The minimum proportion of fragments in a cell to overlap with a promoter sequence
max_frac_mito	The maximum proportion of fragments in a cell that are mitochondrial

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.