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Generates synthetic bulk RNAseq data

synthetic_bulk_cor_matrix.Rd

Function generates synthetic bulkRNAseq data with heteroskedasticity (lowly expressed genes show higher variance) and can optionally add gene ~ gene correlations for testing purposes of module detection methods.

Usage

synthetic_bulk_cor_matrix(
  num_samples = 100L,
  num_genes = 1000L,
  add_modules = TRUE,
  module_sizes = c(100L, 100L, 100L),
  seed = 123L
)

Arguments

num_samples

Integer. Number of samples.

num_genes

Integer. Number of genes.

add_modules

Boolean. Shall gene modules with correlation structures be generated.

module_sizes

Integer vector. Sizes of the different correlation modules. The sum needs be smaller than num_genes.

seed

Integer. Seed for reproducibility purposes.

Value

A synthetic_bulk_data class containing:

  • counts - The count matrix

  • sparse_counts - A slot for sparse counts that can be added later, see simulate_dropouts().

  • module_data - The module membership of the genes