cycle_npreg_loglik: Infer Angles or Cell Cycle Phase Using Gene Expression Data

In jhsiao999/peco: A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data

Description

Infer Angles or Cell Cycle Phase Using Gene Expression Data

Usage

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.

Value

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.

jhsiao999/peco documentation built on Nov. 21, 2020, 5:34 p.m.