weightedCondLogLikDerDelta {edgeR} | R Documentation

## Weighted Conditional Log-Likelihood in Terms of Delta

### Description

Weighted conditional log-likelihood parameterized in terms of delta (`phi / (phi+1)`) for a given gene, maximized to find the smoothed (moderated) estimate of the dispersion parameter

### Usage

    weightedCondLogLikDerDelta(y, delta, tag, prior.n=10, ntags=nrow(y[[1]]), der=0)

### Arguments

`y` | list with elements comprising the matrices of count data (or pseudocounts) for the different groups
`delta` | delta (`phi / (phi+1)`)parameter of negative binomial
`tag` | gene at which the weighted conditional log-likelihood is evaluated
`prior.n` | smoothing paramter that indicates the weight to put on the common likelihood compared to the individual gene's likelihood; default `10` means that the common likelihood is given 10 times the weight of the individual gene's likelihood in the estimation of the genewise dispersion
`ntags` | numeric scalar number of genes in the dataset to be analysed
`der` | derivative, either 0 (the function), 1 (first derivative) or 2 (second derivative)

### Details

This function computes the weighted conditional log-likelihood for a given gene, parameterized in terms of delta. The value of delta that maximizes the weighted conditional log-likelihood is converted back to the `phi` scale, and this value is the estimate of the smoothed (moderated) dispersion parameter for that particular gene. The delta scale for convenience (delta is bounded between 0 and 1). Users should note that ‘tag’ and ‘gene’ are synonymous when interpreting the names of the arguments for this function.

### Value

numeric scalar of function/derivative evaluated for the given gene and delta

### Author(s)

Mark Robinson, Davis McCarthy

### Examples

    counts<-matrix(rnbinom(20,size=1,mu=10),nrow=5)
    d<-DGEList(counts=counts,group=rep(1:2,each=2),lib.size=rep(c(1000:1001),2))
    y<-splitIntoGroups(d)
    ll1<-weightedCondLogLikDerDelta(y,delta=0.5,tag=1,prior.n=10,der=0)
    ll2<-weightedCondLogLikDerDelta(y,delta=0.5,tag=1,prior.n=10,der=1)

[Package edgeR version 3.24.3 Index]