simulateContamination: Simulate contaminated count matrix

In campbio/celda: CEllular Latent Dirichlet Allocation

Simulate contaminated count matrix

Description

This function generates a list containing two count matrices – one for real expression, the other one for contamination, as well as other parameters used in the simulation which can be useful for running decontamination.

Usage

simulateContamination(
  C = 300,
  G = 100,
  K = 3,
  NRange = c(500, 1000),
  beta = 0.1,
  delta = c(1, 10),
  numMarkers = 3,
  seed = 12345
)

Arguments

C	Integer. Number of cells to be simulated. Default 300.
G	Integer. Number of genes to be simulated. Default 100.
K	Integer. Number of cell populations to be simulated. Default 3.
NRange	Integer vector. A vector of length 2 that specifies the lower and upper bounds of the number of counts generated for each cell. Default c(500, 1000).
beta	Numeric. Concentration parameter for Phi. Default 0.1.
delta	Numeric or Numeric vector. Concentration parameter for Theta. If input as a single numeric value, symmetric values for beta distribution are specified; if input as a vector of lenght 2, the two values will be the shape1 and shape2 paramters of the beta distribution respectively. Default c(1, 5).
numMarkers	Integer. Number of markers for each cell population. Default 3.
seed	Integer. Passed to with_seed. For reproducibility, a default value of 12345 is used. If NULL, no calls to with_seed are made.

Value

A list containing the nativeMatirx (real expression), observedMatrix (real expression + contamination), as well as other parameters used in the simulation.

Author(s)

Shiyi Yang, Yuan Yin, Joshua Campbell

Examples

contaminationSim <- simulateContamination(K = 3, delta = c(1, 10))

campbio/celda documentation built on April 5, 2024, 11:47 a.m.