create_synthetic: Create synthetic data

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

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()

mfa documentation built on Nov. 8, 2020, 8:10 p.m.