generateDataSymSim: Generate single cell data using SymSim model

In pengminshi/MRtree: Multi-resolution Reconciled Tree

Generate single cell data using SymSim model

Description

Generate single cell data using SymSim model

Usage

generateDataSymSim(
  ncells,
  ngenes,
  tree,
  params = NULL,
  seed = 42,
  plot.tsne = FALSE,
  ...
)

Arguments

ncells	scalar, number of cells
ngenes	scalar, number of genes
tree	a phylo object specifying the tree struction where the cell type follow
params	a list containing the simulation parameters used in SymSim
seed	random seed
plot.tsne	boolean whether to generate tsne plot
...	other parameters passed to SymSim function

Value

A list of

count

ncell-by-ngene count matrix

params

simulation parameters

true_counts

ncell-by-ngene count matrix without noise and dropouts

gene_len

tsne_true_counts

tSNE plot of the true counts

tsne_UMI_counts

tSNE plot of the simulated observed counts

metadata

Information of the cells

pengminshi/MRtree documentation built on March 6, 2023, 4:20 p.m.