Description Usage Arguments Value Author(s)
View source: R/np_cell_ordering_class.R
The function runs a Gibbs sampler for a number of iterations to obtain the estimates of cell times on cell cycle (modulo rotation) as well as the gene features (smoothing fit)
1 2 | np_cell_ordering_class(cycle_data, celltime_levels, num_iter,
method = c("LOESS", "B-spline", "Wavelet"), save_path = NULL)
|
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 |
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. |
Returns a list containing the following items
cell_times |
estimated cell times from Gibbs sampler |
sigma |
The estimated non-signal or noise 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
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