filterDoublets: filterDoublets

In plantformatics/Socrates: Analysis of scATAC-seq data

filterDoublets

Description

This function identifies potential doublets. A new column in the meta slot (d.type) denotes the doublet status. Doublets can also be directly filtered from the data set by setting removeDoublets to TRUE.

Usage

filterDoublets(
  obj = NULL,
  filterRatio = 1.5,
  embedding = "UMAP",
  libraryVar = NULL,
  verbose = T,
  umap_slotname = "UMAP",
  svd_slotname = "PCA",
  removeDoublets = F
)

Arguments

obj	Socrates object. For best results, use downstream of the function cleanCells prior to normalization.
filterRatio	Numeric. Defaults to 1.5.
embedding	Character string. Which embedding to use for doublet estimation filtering. Defaults to "UMAP".
libraryVar	Character string. Meta data column containing library information. Defaults to NULL, which is specifically for single library/replicate objects. Users with multiple libraries/replicates in the object must set the libraryVar parameter to the column name specifying each cells library ID. The default column name used by mergeSocratesRDS is "sampleID".
verbose	Boolean. Defaults to TRUE.
umap_slotname	Character string. Defaults to "UMAP".
svd_slotname	Character string. Defaults to "PCA".
removeDoublets	Boolean. Defaults to FALSE.

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