bump_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

The function runs a Gibbs sampler for a number of iterations to obtain the estimates of cell times (modulo rotation) when the genes vary as per a bump functin. The function also returns gene features (amplitude, phase and noise variation)

Usage

bump_cell_ordering_class(cycle_data, celltime_levels = 100, num_iter = 100,
  save_path = NULL, start = NULL, verbose = FALSE)

Arguments

num_iter	The number of iterations to run for the Gibbs sampler scheme
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
start	the starting time slots of the cells.
verbose	if TRUE, prints the loglikelihood at each step/iteration. If FALSE,just prints final loglikelihood.
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.

Value

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

Author(s)

Kushal K Dey

kkdey/cellcycleR documentation built on May 20, 2019, 10:33 a.m.