scaden_simulate: Simulates training data from scRNA data

In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

Simulates training data from scRNA data

Description

Simulates training data from scRNA data

Usage

scaden_simulate(
  cell_type_annotations,
  gene_labels,
  single_cell_object,
  temp_dir = NULL,
  cells = 100,
  samples = 1000,
  dataset_name = "scaden",
  verbose = FALSE
)

Arguments

cell_type_annotations	Vector of celltype labels. Order corresponds to rows in single_cell_object matrix.
gene_labels	Vector of gene labels. Order corresponds to columns in single_cell_object matrix.
single_cell_object	Matrix or dataframe of scRNA data. Rows=cells and columns=genes
temp_dir	The temporary directory to use for the computations (optional)
cells	Bulk simulation: Number of cells per sample (default: 100)
samples	Bulk simulation: Number of samples to simulate (default: 1000)
dataset_name	Name of dataset
verbose	Whether to produce an output on the console. (default: false)

Value

Simulated bulk data of known cell type fractions

PelzKo/immunedeconv2 documentation built on Feb. 12, 2025, 4:16 p.m.