cycle_npreg_loglik: Infer angles or cell cycle phase based on gene expression...

In peco: A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

Description

Infer angles or cell cycle phase based on 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 to be selected along 0 to 2pi.
method.grid	The approach to initialize angles in the computation. uniform creates k equally-spaced bins (grids). pca uses gene expression values to infer angles, and then use these pca-based angles to move the cells to the closest bin (as defined by uniform).

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 belong to each bin.

Author(s)

Joyce Hsiao

See Also

initialize_grids for selecting angles in cycle_npreg_loglik, cycle_npreg_mstep for estimating cyclic functions given inferred phases from cycle_npreg_loglik, cycle_npreg_outsample for predicting cell cycle phase using parameters learned from cycle_npreg_insample

Other peco classifier functions: cycle_npreg_insample, cycle_npreg_mstep, cycle_npreg_outsample, initialize_grids

peco documentation built on Nov. 8, 2020, 8:16 p.m.