simulate_sample: simulate single pseudo-bulk sample

In omnideconv/SimBu: Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

simulate single pseudo-bulk sample

Description

function to sample cells according to given cell-type fractions. This creates a single pseudo-bulk sample by calculating the mean expression value per gene over all sampled cells. Note: if total_read_counts is used, the cell-fractions are applied to the number of counts, not the number of cells!

Usage

simulate_sample(
  data,
  scaling_vector,
  simulation_vector,
  total_cells,
  total_read_counts,
  remove_bias_in_counts,
  remove_bias_in_counts_method,
  norm_counts,
  seed
)

Arguments

data	SummarizedExperiment object
scaling_vector	vector with scaling values for each cell; calculated by the calc_scaling_vector function
simulation_vector	named vector with wanted cell-types and their fractions
total_cells	numeric; number of total cells for this simulation
total_read_counts	numeric; sets the total read count value for each sample
remove_bias_in_counts	boolean; if TRUE (default) the internal mRNA bias that is present in count data will be removed using the number of reads mapped to each cell
remove_bias_in_counts_method	'read-number' (default) or 'gene-number'; method with which the mRNA bias in counts will be removed
norm_counts	boolean; if TRUE the samples simulated with counts will be normalized to CPMs, default is FALSE
seed	numeric; fix this value if you want the same cells to be sampled

Value

returns two vectors (one based on counts, one based on tpm; depends on which matrices are present in data) with expression values for all genes in the provided dataset

omnideconv/SimBu documentation built on May 5, 2024, 12:33 p.m.