kersplatSimPaths {splatter} | R Documentation

## Simulate Kersplat paths

### Description

Simulate gene means for each step along each path of a Kersplat simulation

### Usage

    kersplatSimPaths(params, verbose)

### Arguments

`params` | KersplatParams object containing simulation parameters.
`verbose` | logical. Whether to print progress messages

### Details

The method of simulating paths is inspired by the method used in the PROSSTT simulation. Changes in expression are controlled by `paths.nPrograms` regulatory programs. Each of the regulatory genes in the gene network has some association with each program. This is analogous to there being changes in the environment (the programs) which are sensed by receptors (regulatory genes) and cause changes in expression downstream. For each path a random walk is generated for each program and the changes passed on to the regulatory genes. At each step the changes propagate through the network according to the weights on edges between genes. This algorithm is fairly simple but should result in correlation relationships between genes. However it is likely to be improved and adjusted in the future.

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.

### Value

KersplatParams object with path means

### References

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.

[Package splatter version 1.12.0 Index]