Generate simulated RNA-seq data for testing purposes

Simulate an RNASeq count matrix. Adapted from edgeR documentation. This function is not meant for any serious modelling. It's really used mostly for testing plotting and summarizing functions internally. It's good for generating test data.

Usage

simulate_counts(
  n_genes = 1000,
  n_up = 50,
  n_down = 50,
  n_samples = 6,
  groups = c("ctl", "trt"),
  de_group = "trt",
  mu = 10,
  phi = 0.1,
  count_offset = 10
)

Arguments

n_genes

integer. The number of gene to simulate

n_up

integer. The number of genes the count offset will be added to

n_down

integer. the number of genes the count offset will be subtracted from. Negative numbers will be coerced to zeros.

n_samples

integer. The number of samples to simulate

groups

character vector. Character vector specifying the names of the groups to simulate

de_group

character. The name of the group to be differentially expressed

mu

numeric. Mean value of counts

phi

numeric. Dispersion parameter

count_offset

numeric. Count offset to be applied to the up/down genes.

Value

list containing the count matrix and a vectors indicating which rows were modified.

Examples

# simulate counts using default parameters
sim <- simulate_counts()

# extract the count matrix from the simulation result
counts <- sim$table

# show rows where counts were modified
counts[sim$de_genes, ]
#>      ctl.1 ctl.2 ctl.3 trt.1 trt.2 trt.3