condLogLikDerSize {edgeR} | R Documentation

## Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries

### Description

Derivatives of the negative-binomial log-likelihood with respect to the dispersion parameter for each gene, conditional on the mean count, for a single group of replicate libraries of the same size.

### Usage

    condLogLikDerSize(y, r, der=1L)
    condLogLikDerDelta(y, delta, der=1L)

### Arguments

`y` | matrix of counts, all counts in each row having the same population mean
`r` | numeric vector or scalar, size parameter of negative binomial distribution, equal to 1/dispersion
`delta` | numeric vector or scalar, delta parameter of negative binomial, equal to dispersion/(1+dispersion)
`der` | integer specifying derivative required, either 0 (the function), 1 (first derivative) or 2 (second derivative)

### Details

The library sizes must be equalized before running this function. This function carries out the actual mathematical computations for the conditional log-likelihood and its derivatives, calculating the conditional log-likelihood for each gene. Derivatives are with respect to either the size (`r`) or the delta parametrization (`delta`) of the dispersion.

### Value

vector of row-wise derivatives with respect to `r` or `delta`

### Author(s)

Mark Robinson, Davis McCarthy, Gordon Smyth

### Examples

    y <- matrix(rnbinom(10,size=1,mu=10),nrow=5)
    condLogLikDerSize(y,r=1,der=1)
    condLogLikDerDelta(y,delta=0.5,der=1)

[Package edgeR version 3.20.9 Index]