SnapATAC_runScrublet: Doublet removement using Scrublet

In beyondpie/smmtools: Single-cell multi-omics sequenceing data tools

Doublet removement using Scrublet

Description

GMM is used by Kai Zhang in his Cell ATAC Atlas paper. NormalMixEM is used by Yang Li in his CEMBA 1.0

Usage

SnapATAC_runScrublet(
  mat,
  path_to_python,
  expected_doublet_rate = 0.08,
  min_counts = 3,
  min_cells = 5L,
  min_conv_pctl = 85,
  n_pc = 30L
)

Arguments

mat	sparse matrix, cell by feature
path_to_python	string
expected_doublet_rate	double, default is 0.08
min_counts	numeric, default is 3
min_cells	integer, default is 5
min_conv_pctl	numeric, default is 85
n_pc	integer, default is 30

Value

list, five fields

• thresGMM: threshold based on GMM for simulation scores

• thresScrublet: threshold estimated from Scrublets

• probs: probs of real data based on GMM

• scrubletScore: doublet scores of real data based on Scrublets

• simuScrubletScore: doublet scores of simulation data based on Scrublets

• thresMixEM: threshold based normalmixEM for simulation scores.

beyondpie/smmtools documentation built on July 1, 2022, 4:33 a.m.