kersplatSimCellMeans: Simulate Kersplat cell means

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

Simulate Kersplat cell means

Description

Simulate endogenous counts for each cell in a Kersplat simulation

Usage

kersplatSimCellMeans(sim, params, verbose)

Arguments

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

Details

Cells are first assigned to a path and a step along that path. This is controlled by the cells.design parameter which is a data.frame with the columns "Path", "Probability", "Alpha" and "Beta". The Path field is an ID for each path and the Probability field is the probability that a cell will come from that path (must sum to 1). The Alpha and Beta parameters control the density of cells along the path. After they are assigned to paths the step for each cell is sampled from a Beta distribution with parameters shape1 equals Alpha and shape2 equals beta. This approach is very flexible and allows almost any distribution of cells along a path. The distribution can be viewed using hist(rbeta(10000, Alpha, Beta), breaks = 100). Some useful combinations of parameters are:

Alpha = 1, Beta = 1

Uniform distribution along the path

Alpha = 0, Beta = 1

All cells at the start of the path.

Alpha = 1, Beta = 0

All cells at the end of the path.

Alpha = 0, Beta = 0

Cells only at each end of the path.

Alpha = 1, Beta = 2

Linear skew towards the start of the path

Alpha = 0.5, Beta = 1

Curved skew towards the start of the path

Alpha = 2, Beta = 1

Linear skew towards the end of the path

Alpha = 1, Beta = 0.5

Curved skew towards the end of the path

Alpha = 0.5, Beta = 0.5

Curved skew towards both ends of the path

Alpha = 0.5, Beta = 0.5

Curved skew away from both ends of the path

Once cells are assigned to paths and steps the correct means are extracted from the paths.means parameter and adjusted based on each cell's library size. An adjustment for BCV is then applied. Doublets are also simulated at this stage by selecting two path/step combinations and averaging the means.

Value

SingleCellExperiment with cell means

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.