# NumericUtilities: Numeric Utilities In seriph78/COTAN: COexpression Tables ANalysis

 NumericUtilities R Documentation

## Numeric Utilities

### Description

A set of function helper related to the statistical model underlying the COTAN package

### Usage

funProbZero(dispersion, mu)

dispersionBisection(
sumZeros,
lambda,
nu,
threshold = 0.001,
maxIterations = 100L
)

parallelDispersionBisection(
genes,
sumZeros,
lambda,
nu,
threshold = 0.001,
maxIterations = 100L
)

nuBisection(
sumZeros,
lambda,
dispersion,
initialGuess,
threshold = 0.001,
maxIterations = 100L
)

parallelNuBisection(
cells,
sumZeros,
lambda,
dispersion,
initialGuess,
threshold = 0.001,
maxIterations = 100L
)


### Arguments

 dispersion the estimated dispersion (a n-sized vector) mu the lambda times nu values (a n \times m matrix) sumZeros the number of genes not expressed in the relevant cell (a m-sized vector) lambda the estimated lambda (a n-sized vector) nu the estimated nu (a m-sized vector) threshold minimal solution precision maxIterations max number of iterations (avoids infinite loops) genes names of the relevant genes initialGuess the initial guess for nu (a m-sized vector) cells names of the relevant cells

### Details

funProbZero is a private function that gives the probability that a sample gene's reads are zero, given the dispersion and mu parameters.

Using d for disp and \mu for mu, it returns: (1 + d \mu)^{-\frac{1}{d}} when d > 0 and \exp{((d - 1) \mu)} otherwise. The function is continuous in d = 0, increasing in d and decreasing in \mu. It returns 0 when d = -\infty or \mu = \infty. It returns 1 when \mu = 0.

dispersionBisection is a private function for the estimation of dispersion slot of a COTAN object via a bisection solver

The goal is to find a dispersion value that reduces to zero the difference between the number of estimated and counted zeros

parallelDispersionBisection is a private function invoked by estimateDispersionBisection() for the estimation of the dispersion slot of a COTAN object via a parallel bisection solver

The goal is to find a ⁠dispersion array⁠ that reduces to zero the difference between the number of estimated and counted zeros

nuBisection is a private function for the estimation of nu slot of a COTAN object via a bisection solver

The goal is to find a nu value that reduces to zero the difference between the number of estimated and counted zeros

parallelNuBisection is a private function invoked by estimateNuBisection() for the estimation of nu slot of a COTAN object via a parallel bisection solver

The goal is to find a ⁠nu array⁠ that reduces to zero the difference between the number of estimated and counted zeros

### Value

the probability matrix that a read count is identically zero

the dispersion value

the dispersion values

the nu value

the dispersion values

seriph78/COTAN documentation built on July 2, 2024, 9:27 a.m.