cycle_npreg_loglik {peco} | R Documentation

## Infer angles or cell cycle phase based on gene expression 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`

[Package peco version 0.99.16 Index]