escoSimTrueCounts: Simulate true counts

In JINJINT/splattermodify: Simple Simulation of Single-cell RNA Sequencing Data

Description

Simulate a true counts matrix. Counts are simulated from a poisson distribution where each gene in each cell has it's own mean based on the group (or path position), expected library size and BCV. Additional gene-gene interaction can be introduced via a copula model with correlation matrix input by design or randomly generated from a real purifed gene expression data set from NeuroExpresso https://www.eurekalert.org/pub_releases/2017-11/sfn-nwa111417.php.

Usage

escoSimTrueCounts(sim, type, verbose, numCores = 2)

Arguments

sim	SingleCellExperiment to add true counts to.
type	The type of cell structure: 'single', 'group', 'tree', or 'traj'.
verbose	whether to print the process or not
numCores	the number of cores for parallelization during simulation, if set as NULL, then all the cores are used.

Value

sim SingleCellExperiment with simulated true counts.

JINJINT/splattermodify documentation built on May 19, 2021, 4:05 p.m.