SCCellFilter: Filtering valid single cells

SCCellFilterR Documentation

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/wzzw documentation built on Aug. 13, 2022, 7:11 a.m.