simulate_twoOmicsData {SUMO}R Documentation

Simulation of omics with predefined single or multiple latent factors in multi-omics

Description

Simulates two high-dimensional omics datasets with customizable latent factor structures. Users can control the number and type of factors (shared, unique, mixed), the signal-to-noise ratio, and the distribution of signal-carrying samples and features. The function is flexible for benchmarking multi-omics integration methods under various controlled scenarios.

Usage

simulate_twoOmicsData(
  vector_features = c(2000, 2000),
  n_samples = 50,
  n_factors = 3,
  signal.samples = NULL,
  signal.features.one = NULL,
  signal.features.two = NULL,
  num.factor = "multiple",
  snr = 1,
  advanced_dist = NULL,
  ...
)

Arguments

vector_features

A numeric vector of length two, specifying the number of features in the first and second omics datasets, respectively.

n_samples

Integer. The number of samples shared between both omics datasets.

n_factors

Integer. Number of latent factors to simulate.

signal.samples

Optional numeric vector of length two: the first element is the mean, and the second is the variance of the number of signal-carrying samples per factor. If NULL, signal assignment is inferred from snr.

signal.features.one

Optional numeric vector of length two: the first element is the mean, and the second is the variance of the number of signal-carrying features per factor in the first omic.

signal.features.two

Optional numeric vector of length two: the first element is the mean, and the second is the variance of the number of signal-carrying features per factor in the second omic.

num.factor

Character string. Either 'single' or 'multiple'. Determines whether to simulate a single latent factor or multiple factors.

snr

Numeric. Signal-to-noise ratio used to estimate the background noise. The function uses this value to infer the proportion of signal versus noise in the simulated datasets.

advanced_dist

Character string. Specifies how latent factors are distributed when num.factor = 'multiple'. Options include: ”, NULL, 'mixed', 'omic.one', 'omic.two', or 'exclusive'.

...

Additional arguments (not currently used).


[Package SUMO version 1.2.0 Index]