Inferring a trajectory inference using SCIMITAR

Source: R/ti_scimitar.R

Will generate a trajectory using SCIMITAR.

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

ti_scimitar(covariance_type = "diag", degree = 3L, step_size = 0.07,
  cov_estimator = "corpcor", cov_reg = 0.05, max_iter = 3L,
  run_environment = NULL)

Arguments

covariance_type

discrete; (default: "diag"; values: "diag", "spherical", "full")
degree

integer; (default: 3L; range: from 1L to 20L)
step_size

numeric; (default: 0.07; range: from 0.01 to 0.1)
cov_estimator

discrete; (default: "corpcor"; values: "identity", "diag", "sample", "global", "glasso", "corpcor", "average")
cov_reg

numeric; (default: 0.05; range: from 0.01 to 0.1)
max_iter

integer; (default: 3L; range: from 1L to 20L)
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

CORDERO, P., STUART, J.M., 2016. TRACING CO-REGULATORY NETWORK DYNAMICS IN NOISY, SINGLE-CELL TRANSCRIPTOME TRAJECTORIES. Biocomputing 2017.