fitNBtbCl: Function for fitting a negative binomial noise model of...

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Function for fitting a negative binomial noise model of technical and biological variability

Description

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. Local mean and and global cell-to-cell variability of transcript counts are pre-computed arguments.

Usage

fitNBtbCl(z, mu, rt, gamma = 2, x0 = 0.1, lower = 0, upper = 100)

Arguments

z	Transcript count matrix with cells as columns and genes as rows.
mu	Vector of mean expression values across cells in z.
rt	Vector of dispersion parameters explaining global cell-to-cell variability of transcript counts across cells in z.
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.

Value

Vector of biological noise parameters across cells in z.

RaceID documentation built on Sept. 28, 2023, 5:06 p.m.