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.
1 2 3 |
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 |
Kushal K Dey, Joyce Hsiao
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.