Inferring a trajectory inference using MERLoT

Will generate a trajectory using MERLoT.

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

ti_merlot(sigma = "local", distance = "euclidean", ndim = 20L,
  density_norm = TRUE, n_local_lower = 5L, n_local_upper = 7L,
  w_width = 0.01, n_components_to_use = 3, N_yk = 100,
  lambda_0 = 1e-10, mu_0 = 0.0025, increaseFactor_mu = 20,
  increaseFactor_lambda = 20, FixEndpoints = FALSE,
  run_environment = NULL)

Arguments

sigma	discrete; Diffusion scale parameter of the Gaussian kernel. A larger sigma might be necessary if the eigenvalues can not be found because of a singularity in the matrix. Must be one of: a numeric global sigma -- a global sigma will be calculated using destiny::find_sigmas() or a destiny::Sigmas-class() object. (default: "local"; values: "local", "global")
distance	discrete; A stats::dist() object, or a character vector specifying which distance metric to use. Allowed measures: cosine distance (1-corr(c_1, c_2)), or rank correlation distance (1-corr(rank(c_1), rank(c_2))) (default: "euclidean"; values: "euclidean", "cosine", "rankcor")
ndim	integer; Number of eigenvectors/dimensions to return (default: 20L; range: from 2L to 20L)
density_norm	logical; Logical. If TRUE, use density normalisation
n_local_lower	integer; If sigma == 'local', the n_local_lower:n_local_upper nearest neighbor(s) determine(s) the local sigma (default: 5L; range: from 2L to 20L)
n_local_upper	integer; See n_local_lower (default: 7L; range: from 2L to 20L)
w_width	numeric; Window width to use for deciding the branch cutoff (default: 0.01; range: from 1e-04 to 1)
n_components_to_use	integer; Which components to use in downstream analysis (default: 3; range: from 2 to 20)
N_yk	integer; Number of nodes for the elastic principal tree (default: 100; range: from 2 to 1000)
lambda_0	numeric; Principal elastic tree energy function parameter. (default: 1e-10; range: from 1e-15 to 1e-04)
mu_0	numeric; Principal elastic tree energy function parameter. (default: 0.0025; range: from 5e-04 to 0.005)
increaseFactor_mu	numeric; Factor by which the mu will be increased for the embedding (default: 20; range: from 2 to 50)
increaseFactor_lambda	numeric; Factor by which the mu will be increased for the embedding (default: 20; range: from 2 to 50)
FixEndpoints	logical; Documentation not provided by authors
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

Parra, R.G., Papadopoulos, N., Ahumada-Arranz, L., El Kholtei, J., Treutlein, B., Soeding, J., 2018. Reconstructing complex lineage trees from scRNA-seq data using MERLoT.