create_synthetic: Create synthetic data

In kieranrcampbell/mfa: Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations

Create synthetic data

Description

Create synthetic bifurcating data for two branches. Optionally incorporate zero inflation and transient gene expression.

Usage

create_synthetic(C = 100, G = 40, p_transient = 0, zero_negative = TRUE,
  model_dropout = FALSE, lambda = 1)

Arguments

C	Number of cells to simulate
G	Number of genes to simulate
p_transient	Propotion of genes that exhibit transient expression
zero_negative	Logical: should expression generated less than zero be set to zero? This will zero-inflate the data
model_dropout	Logical: if true, expression will be set to zero with the exponential dropout formula dependent on the latent expression using dropout parameter lambda
lambda	The dropout parameter

Value

A list with the following entries:

• X A cell-by-feature expression matrix

• branch A vector of length C assigning cells to branches

• pst A vector of pseudotimes for each cell

• k The k parameters

• phi The φ parameters

• delta The δ parameters

• p_transient The proportion of genes simulated as transient according to the original function call

Examples

synth <- create_synthetic()

kieranrcampbell/mfa documentation built on March 27, 2022, 5:20 a.m.