initialize_grids {peco} | R Documentation

## For prediction, initialize grid points for cell cycle phase on a circle.

### Description

For prediction, initialize grid points for cell cycle phase on a circle.

### Usage

    initialize_grids(Y, grids = 100, method.grid = c("pca", "uniform"))

### Arguments

`Y` | Gene expression matrix. Gene by sample.
`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 vector of initialized angles to be used in `cycle_npreg_loglik` to infer angles.

### Author(s)

Joyce Hsiao

### See Also

`cycle_npreg_loglik` for log-likehood at angles between 0 to 2pi, `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_loglik`, `cycle_npreg_mstep`, `cycle_npreg_outsample`

[Package peco version 1.6.0 Index]