View source: R/VarID_functions.R
fitNBtb | R Documentation |
This function fits a negative binomial model to transcript counts of a group of cells thereby deconvoluting variability into sampling noise, global cell-to-cell variability of transcript counts, and residual variability, which corresponds to biological noise.
fitNBtb(z, gamma = 2, x0 = 0, lower = 0, upper = 100, grad = TRUE)
z |
Transcript count matrix with cells as columns and genes as rows. |
gamma |
Positive real number. Scale paramter of the cauchy prior. Default is 2. |
x0 |
Real number greater or equal to zero. Location parameter of the cauchy prior. |
lower |
Real number greater or equal to zero. Lower bound for the maximum a posterior inference of the biological noise. Default is 0. |
upper |
Real number greater or equal to zero. Upper bound for the maximum a posterior inference of the biological noise. Default is 100. |
grad |
Logical. If |
Data.frame with four columns:
mu |
Mean expression. |
epsilon |
Biological noise. |
rt |
Dispersion parameter capturing global cell-to-cell variability of transcript counts. |
alphaG |
Dispersion parameter capturing global cell-to-cell variability of transcript counts and biological noise. |
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