simulate_experiment: Simulate a DECAL perturbation experiment

In mauranolab/decal: Differential Expression Analysis of Clonal Alterations Local effects

Description

It simulates a random DECAL experiment generating a random UMI count matrix with cells randomly assigned to different clones and introducing to each clone perturbations to random genes.

Usage

sim_experiment(
  depth,
  ratio,
  lfc = 0,
  nclones = 10L,
  min_n = 2L,
  max_n = 20L,
  theta = 100L
)

sim_experiment_from_data(
  reference,
  lfc = 0,
  nclones = 10L,
  min_n = 2L,
  max_n = 20L,
  theta = 100L,
  ngenes = NULL
)

Arguments

depth	cells total UMI count
ratio	ratio of genes UMI over total UMI count
lfc	vector indicating the perturbations to be generated for each clone
nclones	number of clones to be simulated
min_n	minimum clone size
max_n	maximum clone size
theta	negative binomial dispersion parameter
reference	UMI count matrix used as base for the simulation
ngenes	number of genes to be simulated. When NULL it replicates the gene ratio found in reference, otherwise it simulates ngenes with ratio ranging in a logarithm scale from lowest to highest observed ratio observed.

Value

a list containing the following fields:

• perturbations, a table indicating the perturbations expected_lfc for a gene in a clone.

• clone, a list of cells assigned to each clone.

• count, a random UMI count matrix.

mauranolab/decal documentation built on Dec. 21, 2021, 3:50 p.m.