sin_cell_ordering_class: Cell ordering into different phases on the cell cycle using...
In kkdey/cellcycleR: For ordering the single cells on the cell cycle

Description Usage Arguments Value Author(s)

View source: R/sin_cell_ordering_class.R

This function fits a sinsoidal model to gene expression data and computes cell-order estimates on cell-cycle (modulo rotation), as well as the gene-specific cell-cycle features, including amplitude, phase and noise variation.

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sin_cell_ordering_class(cycle_data, celltime_levels, num_iter = NULL,
  save_path = NULL, fix.phase = FALSE, phase_in = NULL, verbose = FALSE,
  tol = 0.01, maxiter = 500)

`cycle_data`	a N x G matrix, where N is number of cells, G number of genes
`celltime_levels`	The number of phase classes chosen (The deafult is 100). It splits up circle or the range (0, 2pi) into celltime_levels uniform splits.
`num_iter`	Number of iterations. If not specified, number of iteration is set to be maxiter (the maximum number of iteratoins).
`save_path`	The file path to save the RDA file containing the information on gene characteristics and the cell ordering times. Default is NULL in which case, it will not save output
`fix.phase`	if TRUE, the phase will be fixed in inference for the genes, default is FALSE
`phase_in`	if fix.phase is TRUE, then phase_in is G x 1 vector of user input gene phases. Default is NULL as is the case if fix.phase=FALSE.
`verbose`	if TRUE, prints the loglikelihood at each step/iteration. If FALSE,just prints final loglikelihood.
`maxiter`	The maximum number of iterations. Default = 500.
`freq`	The frequency of the sinusoidal genes. The default is 1.

Returns a list containing the following items

`cell_times`	estimated cell times from Gibbs sampler
`amp`	The estimated amplitudes of the genes
`phi`	The estimated phase angles of the genes
`sigma`	The estimated non sinusoid signal variation of the genes
`loglik`	The model log likelihood of the fit
`signal_intensity`	The intensity of each cell in each of the cell times classes