Inferring a trajectory inference using FORKS

Will generate a trajectory using FORKS.

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

ti_forks(norm_function = "median", norm_quantile = 75L,
  cum_sum_exp_var = 0.9, min_cluster = 4L, max_cluster = 10L,
  mapping_type = "Isomap", initialization = "kmeans",
  iterMax = 1000L, eta = 0.01, C = 1L, run_environment = NULL)

Arguments

norm_function	discrete; No description provided by the author. (default: "median"; values: "mean", "median", "quantile")
norm_quantile	numeric; No description provided by the author. (default: 75L; range: from 0L to 100L)
cum_sum_exp_var	numeric; No description provided by the author. (default: 0.9; range: from 0 to 1)
min_cluster	integer; No description provided by the author. (default: 4L; range: from 3L to 20L)
max_cluster	integer; No description provided by the author. (default: 10L; range: from 3L to 20L)
mapping_type	discrete; No description provided by the author. (default: "Isomap"; values: "Isomap", "MDS", "PCA", "RandomForest", "SpectralEmbedding", "LLE_standard", "tSNE")
initialization	discrete; No description provided by the author. (default: "kmeans"; values: "kmeans", "kmedoids", "random")
iterMax	integer; No description provided by the author. (default: 1000L; range: from 100L to 100000L)
eta	numeric; No description provided by the author. (default: 0.01; range: from 1e-04 to 100L)
C	numeric; No description provided by the author. (default: 1L; range: from 1e-04 to 1000L)
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

Sharma, M., Li, H., Sengupta, D., Prabhakar, S., Jayadeva, J., 2017. FORKS: Finding Orderings Robustly using K-means and Steiner trees.