PhenoPath simulation

Simulate counts from a pseudotime trajectory using the PhenoPath method.

phenoSimulate(params = newPhenoParams(), verbose = TRUE, ...)

Arguments

params	PhenoParams object containing simulation parameters.
verbose	logical. Whether to print progress messages
...	any additional parameter settings to override what is provided in params.

Value

SingleCellExperiment containing simulated counts

Details

This function is just a wrapper around simulate_phenopath that takes a PhenoParams, runs the simulation then converts the output from log-expression to counts and returns a SingleCellExperiment object. The original simulated log-expression values are returned in the LogExprs assay. See simulate_phenopath and the PhenoPath paper for more details about how the simulation works.

References

Campbell K, Yau C. Uncovering genomic trajectories with heterogeneous genetic and environmental backgrounds across single-cells and populations. bioRxiv (2017).

Paper: 10.1101/159913

Code: https://github.com/kieranrcampbell/phenopath

Examples

if (requireNamespace("phenopath", quietly = TRUE)) {
    sim <- phenoSimulate()
}
#> Simulating counts...
#> Warning: `as_data_frame()` is deprecated as of tibble 2.0.0.
#> Please use `as_tibble()` instead.
#> The signature and semantics have changed, see `?as_tibble`.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_warnings()` to see where this warning was generated.
#> Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
#> Using compatibility `.name_repair`.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_warnings()` to see where this warning was generated.
#> Creating final dataset...