SCCellFilter: Filtering valid single cells

In wzthu/ATACFlow: An Easy-to-use Systematic pipeline for ATACseq data analysis

Filtering valid single cells

Description

Filtering valid single cells for downstream aalysis.

Usage

atacSCCellFilter(
  atacProc,
  csvInput = NULL,
  threshold_fragQC1 = 1000,
  threshold_fragQC2 = 45000,
  threshold_nsQC = 4,
  threshold_tssQC = 2,
  threshold_peakQC1 = 3000,
  threshold_peakQC2 = 20000,
  threshold_peakQC3 = 0.15,
  threshold_blacklistQC = 0.05,
  ...
)

## S4 method for signature 'ATACProc'
atacSCCellFilter(
  atacProc,
  csvInput = NULL,
  threshold_fragQC1 = 1000,
  threshold_fragQC2 = 45000,
  threshold_nsQC = 4,
  threshold_tssQC = 2,
  threshold_peakQC1 = 3000,
  threshold_peakQC2 = 20000,
  threshold_peakQC3 = 0.15,
  threshold_blacklistQC = 0.05,
  ...
)

atacscCellFilter(
  csvInput = NULL,
  threshold_fragQC1 = 1000,
  threshold_fragQC2 = 45000,
  threshold_nsQC = 4,
  threshold_tssQC = 2,
  threshold_peakQC1 = 3000,
  threshold_peakQC2 = 20000,
  threshold_peakQC3 = 0.15,
  threshold_blacklistQC = 0.05,
  ...
)

Arguments

atacProc	ATACProc-class object scalar. It has to be the return value of upstream process: SCQC
csvInput	scATAC-seq csv record file.
threshold_fragQC1	Lower bound for fragment count per cell.
threshold_fragQC2	Upper bound for fragment count per cell.
threshold_nsQC	Nucleosome QC threshold (less than).
threshold_tssQC	TSS QC threshold (great than).
threshold_peakQC1	Lower bound for fragment count in peaks.
threshold_peakQC2	Upper bound for fragment count in peaks.
threshold_peakQC3	peak counts ratio (great than).
threshold_blacklistQC	blacklist counts ratio (less than).
...	Additional arguments, currently unused.

Value

An invisible ATACProc-class object scalar.

Author(s)

Wei Zhang

Examples

print(123)

wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.