Infer Angles or Cell Cycle Phase Using Gene Expression Data

cycle_npreg_loglik(
  Y,
  sigma_est,
  funs_est,
  grids = 100,
  method.grid = c("pca", "uniform")
)

Arguments

Y	Gene by sample expression matrix.
sigma_est	A vector of standard errors for each gene from the training data.
funs_est	A vector of cyclic functions estimated for each gene from the training data.
grids	Number of bins used over interval 0 to `2*pi`.
method.grid	The approach used to initialize angles in the computation. `method.grid = "uniform"` creates k equally-spaced bins ("grids"). `method.grid = "pca"` uses gene expression values to infer angles, and then these angles are used to project the cells to the closest bin.

A list with the following three elements:

cell_times_est

Inferred angles or cell cycle phases (not ordered).

loglik_est

Log-likelihood estimates for each gene.

prob_per_cell_by_celltimes

Probabilities of each cell belonging to each bin.