detectDoublets: detectDoublets

In plantformatics/Socrates: Analysis of scATAC-seq data

detectDoublets

Description

This function estimates doublet likelihood via synthetic doublet creation and enrichment analysis. The underlying code is heavily adapted from ArchR described by Granja and Corces et al. If you use detectDoublets in your analysis, please cite the original ArchR paper.

Usage

detectDoublets(
  obj = NULL,
  nTrials = 5,
  nSample = 1000,
  k = 10,
  threads = 1,
  rdMethod = NULL,
  svd_slotName = "PCA"
)

Arguments

obj	Socrates object. For best results, use downstream of the function cleanCells prior to normalization.
nTrials	Numeric. Number of times nSample cells are simulated.
nSample	Numeric. Number of synthetic doublets to create per trial.
k	Numeric. Number of nearest neighbors to search for when estimating doublet enrichment via knn from the narbor package.
threads	Numeric. Number of threads to use for mclapply from the parallel package.
rdMethod	Character. Either "SVD" or "NMF" for dimensionality reduction used previously. Defaults to NULL, using the method specified in obj$rdMethod.
svd_slotName	Character. Slot name containing reduced dimensions from reduceDims function. Default is PCA.

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.