cycle_npreg_insample {peco} | R Documentation

## Obtain cyclic trend estimates from the training data

### Description

Estimates cyclic trends of gene expression levels using training data.

### Usage

    cycle_npreg_insample(Y, theta, ncores = 2, polyorder = 2,
      method.trend = c("trendfilter", "loess", "bspline"))

### Arguments

`Y` | A matrix of normalized and transformed gene expression values. Gene by sample.
`theta` | A vector of angles.
`ncores` | We use doParallel package for parallel computing.
`polyorder` | We estimate cyclic trends of gene expression levels using nonparamtric trend filtering. The default fits second degree polynomials.
`method.trend` | Varous methods that can be applied to estimate cyclic trend of gene expression levels.

### Value

A list with four elements:

`Y` | Gene expression marix.
`theta` | Vector of angles or cell cycle phases.
`sigma_est` | Estimated standard error of the cyclic trend for each gene.
`funs_est` | A list of functions for approximating the cyclic trends of gene express levels for each gene.

### Author(s)

Joyce Hsiao

### See Also

`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_loglik`, `cycle_npreg_mstep`, `cycle_npreg_outsample`, `initialize_grids`

### Examples

    # see \code{\link{cycle_npreg_insample}}

[Package peco version 1.4.0 Index]