simulateCells: Simulate count data from the celda generative models.

In celda: CEllular Latent Dirichlet Allocation

Description

This function generates a SingleCellExperiment containing a simulated counts matrix in the "counts" assay slot, as well as various parameters used in the simulation which can be useful for running celda and are stored in metadata slot. The user must provide the desired model (one of celda_C, celda_G, celda_CG) as well as any desired tuning parameters for those model's simulation functions as detailed below.

Usage

simulateCells(
  model = c("celda_CG", "celda_C", "celda_G"),
  S = 5,
  CRange = c(50, 100),
  NRange = c(500, 1000),
  C = 100,
  G = 100,
  K = 5,
  L = 10,
  alpha = 1,
  beta = 1,
  gamma = 5,
  delta = 1,
  seed = 12345
)

Arguments

model	Character. Options available in celda::availableModels. Can be one of "celda_CG", "celda_C", or "celda_G". Default "celda_CG".
S	Integer. Number of samples to simulate. Default 5. Only used if model is one of "celda_CG" or "celda_C".
CRange	Integer vector. A vector of length 2 that specifies the lower and upper bounds of the number of cells to be generated in each sample. Default c(50, 100). Only used if model is one of "celda_CG" or "celda_C".
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).
C	Integer. Number of cells to simulate. Default 100. Only used if model is "celda_G".
G	Integer. The total number of features to be simulated. Default 100.
K	Integer. Number of cell populations. Default 5. Only used if model is one of "celda_CG" or "celda_C".
L	Integer. Number of feature modules. Default 10. Only used if model is one of "celda_CG" or "celda_G".
alpha	Numeric. Concentration parameter for Theta. Adds a pseudocount to each cell population in each sample. Default 1. Only used if model is one of "celda_CG" or "celda_C".
beta	Numeric. Concentration parameter for Phi. Adds a pseudocount to each feature module in each cell population. Default 1.
gamma	Numeric. Concentration parameter for Eta. Adds a pseudocount to the number of features in each module. Default 5. Only used if model is one of "celda_CG" or "celda_G".
delta	Numeric. Concentration parameter for Psi. Adds a pseudocount to each feature in each module. Default 1. Only used if model is one of "celda_CG" or "celda_G".
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 SingleCellExperiment object with simulated count matrix stored in the "counts" assay slot. Function parameter settings are stored in the metadata slot. For "celda_CG" and "celda_C" models, columns celda_sample_label and celda_cell_cluster in colData contain simulated sample labels and cell population clusters. For "celda_CG" and "celda_G" models, column celda_feature_module in rowData contains simulated gene modules.

Examples

sce <- simulateCells()

celda documentation built on Nov. 8, 2020, 8:24 p.m.