simulate_counts: Generate simulated RNA-seq data for testing purposes

In coriell-research/coriell: Convenience Functions for Bioinformatics

Generate simulated RNA-seq data for testing purposes

Description

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, ]

coriell-research/coriell documentation built on March 29, 2025, 2:19 p.m.