add_miQC: Add miQC model and probability compromised to a...

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

Add miQC model and probability compromised to a SingleCellExperiment object

Description

Add miQC model and probability compromised to a SingleCellExperiment object

Usage

add_miQC(
  sce,
  posterior_cutoff = 0.75,
  keep_all_below_boundary = TRUE,
  enforce_left_cutoff = TRUE,
  seed = NULL
)

Arguments

sce	SingleCellExperiment object.
posterior_cutoff	Optional posterior cutoff used for the miQC filtering calculation (default 0.75)
keep_all_below_boundary	Option to be passed to miQC::filterCells() (default TRUE)
enforce_left_cutoff	Option to be passed to miQC::filterCells() (default TRUE)
seed	An optional random seed for reproducibility.

Value

SingleCellExperiment with prob_compromised column added to colData If the model fits properly, there will also be a miQC_model slot added to the metadata.

AlexsLemonade/scpcaTools documentation built on July 12, 2024, 8:34 a.m.