escoSimTrajDE: Simulate differential expression (DE) factors for trajectory
In JINJINT/ESCO: Simple Simulation of Single-cell RNA Sequencing Data

Description Usage Arguments Details Value References

The DE factor for DE genes are simulated for each step along each path (branches of trajectory)

1	escoSimTrajDE(sim, verbose)

`sim`	SingleCellExperiment to add differential expression to.
`verbose`	logical. Whether to print progress messages

The method of simulating paths is inspired by the method used in the PROSSTT simulation. Changes in expression are controlled by paths.changes regulatory programs. For each path a random walk through paths.diffusion and paths.velocity is generated for each DE genes.

The path structure itself is specified by the paths.design parameter. This is a data.frame with three columns: "Path", "From", and "Steps". The Path field is an ID for each path while the Steps field controls the length of each path. Increasing the number of steps will increase the difference in expression between the ends of the paths. The From field sets the originating point of each path. For example a From of 0, 0, 0 would indicate three paths from the origin while a From of 0, 1, 1 would give a branching structure with Path 1 beginning at the origin and Path 2 and Path 3 beginning at the end of Path 1.

SingleCellExperiment with simulated trajetory means.

Papadopoulos N, Parra RG, Söding J. PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. Bioinformatics (2019). https://doi.org/10.1093/bioinformatics/btz078.

JINJINT/ESCO documentation built on May 13, 2021, 7:25 p.m.