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 |
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 |
... |
Additional arguments (not currently used). |