SketchData: Sketch Data

In satijalab/seurat: Tools for Single Cell Genomics

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,
  ...
)

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 indicating the number of cells to sample for the sketching. 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
...	Arguments passed to other methods

Value

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

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.