SketchData: Sketch Data

Description

This function uses sketching methods to downsample high-dimensional single-cell RNA expression data, which can help with scalability for large datasets.

Usage

SketchData(
  object,
  assay = NULL,
  ncells = 5000L,
  sketched.assay = "sketch",
  method = c("LeverageScore", "Uniform"),
  var.name = "leverage.score",
  over.write = FALSE,
  seed = 123L,
  cast = "dgCMatrix",
  verbose = TRUE,
  features = NULL,
  ...
)

Value

A Seurat object with the sketched data added as a new assay.

Arguments

object: A Seurat object.
assay: Assay name. Default is NULL, in which case the default assay of the object is used.
ncells: A positive integer or a named vector/list specifying the number of cells to sample per layer. If a single integer is provided, the same number of cells will be sampled from each layer. Default is 5000.
sketched.assay: Sketched assay name. A sketch assay is created or overwrite with the sketch data. Default is 'sketch'.
method: Sketching method to use. Can be 'LeverageScore' or 'Uniform'. Default is 'LeverageScore'.
var.name: A metadata column name to store the leverage scores. Default is 'leverage.score'.
over.write: whether to overwrite existing column in the metadata. Default is FALSE.
seed: A positive integer for the seed of the random number generator. Default is 123.
cast: The type to cast the resulting assay to. Default is 'dgCMatrix'.
verbose: Print progress and diagnostic messages
features: A character vector of feature names to include in the sketched assay.
...: Arguments passed to other methods