escoSimTrajMeans: Simulate esco trajetory cell means

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

Description

Simulate esco trajetory cell means

Usage

escoSimTrajCellMeans(sim, verbose)

Arguments

sim	SingleCellExperiment containing simulation.
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 "traj", "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. The distribution can be viewed using hist(rbeta(10000, Alpha, Beta), breaks = 100). 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.

Value

sim SingleCellExperiment with cell means

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