sim_sinusoidal_cycle: Simulate sinusoidal gene expression along cell phases on cell...

In kkdey/cellcycleR: For ordering the single cells on the cell cycle

Description

The function simulates sinusoidal gene patterns over a cell cycle with the cell phases provided by the user.

Usage

sim_sinusoidal_cycle(num_genes, amp_genes, phi_genes, sigma_genes, cell_times,
  correlation = NULL)

Arguments

num_genes	The number of sinusoidal genes to simulate
amp_genes	The amplitude vector of the sinusoidal genes (of length equal to num_genes)
phi_genes	The phase angle vector of the sinusoidal genes (of length equal to num_genes)
sigma_genes	The noise variation vector of the sinusoidal genes (of length equal to num_genes)
cell_times	The phases of the cells on the cell cycle (a vector of values between 0 to 2 pi degrees) The length of cell_times corresponds to number of single cells considered for simulation (say N).

Value

A matrix of size N x num_genes.

Author(s)

Kushal K Dey, Joyce Hsiao

Examples

G <- 500
num_cells <- 400
amp_genes <- rep(10, G)
phi_genes <- runif(G, 0, 2*pi)
sigma_genes <- rchisq(G, 4)
cell_times_sim <- sample(seq(0,2*pi, 2*pi/(num_cells-1)), num_cells, replace=FALSE);

# Assume uncorrelated gene expression
cycle_data <- sim_sinusoidal_cycle(G, amp_genes, phi_genes,
                                   sigma_genes, cell_times_sim,
                                   correlation = NULL)

# Assume correlation gene expression
cycle_data <- sim_sinusoidal_cycle(G, amp_genes, phi_genes,
                                   sigma_genes, cell_times_sim,
                                   correlation = .3)

kkdey/cellcycleR documentation built on May 20, 2019, 10:33 a.m.