kersplatSimLibSizes: Simulate Kersplat library sizes

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

Simulate Kersplat library sizes

Description

Generate library sizes for cells in the Kersplat simulation

Usage

kersplatSimLibSizes(sim, params, verbose)

Arguments

sim	SingleCellExperiment containing simulation.
params	KersplatParams object with simulation parameters.
verbose	logical. Whether to print progress messages

Details

Library sizes are simulated in one of two ways depending on the value of the lib.method parameter.

If lib.method is "fit" (default) then means are sampled from a log-normal distribution with meanlog equals lib.loc and sdlog equals lib.scale.

If mean.method is "density" then library sizes are sampled from the density object in the lib.density parameter using a rejection sampling method. This approach is more flexible but may violate some statistical assumptions.

Ambient library sizes are also generated from a log-normal distribution based on the parameters for the cell library size and adjusted using the ambient.scale parameter.

Value

SingleCellExperiment with library sizes

Oshlack/splatter documentation built on April 1, 2024, 9:37 a.m.