Inferring a trajectory inference using PhenoPath

Source: R/ti_phenopath.R

Will generate a trajectory using PhenoPath.

This method was wrapped inside a container. The original code of this method is available here.

ti_phenopath(thin = 40L, z_init = "1", model_mu = FALSE,
  scale_y = TRUE, run_environment = NULL)

Arguments

thin

integer; The number of iterations to wait each time beforere-calculating the elbo (default: 40L; range: from 2L to 500L)
z_init

discrete; The initialisation of the latent trajectory. Should be one of

  1. A numeric vector of length number of samples to be used directly for initialisation, or

  2. The text character "random", for random initialisation from a standard normal distribution.

(default: "1"; values: "1", "2", "3", "4", "5", "random")
model_mu

logical; Logical - should a gene-specific intercept term be modelled?
scale_y

logical; Logical - should the expression matrix be centre scaled?
run_environment

In which environment to run the method, can be "docker" or "singularity".

Value

A TI method wrapper to be used together with infer_trajectory

References

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