create_synthetic: Create synthetic data

View source: R/mfa.R

create_syntheticR Documentation

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.