logLikDerP {edgeR}R Documentation

Log-likelihood for proportion

Description

Log-likelihood and derivatives for the proportion parameter of negative binomial (mean = library size * proportion)

Usage

logLikDerP(p, y, lib.size, r, der = 0)

Arguments

p vector of proportion parameters to be evaluated
y matrix of data
lib.size vector of library sizes
r size parameter of negative binomial distribution
der derative, either 0 (the function), 1 (first derivative) or 2 (second derivative)

Value

vector of evaluations

Author(s)

Mark Robinson

Examples

y<-matrix(rnbinom(20,size=1.5,mu=10),nrow=5)
d<-list(data=y,group=rep(1:2,each=2),lib.size=rep(c(1000:1001),2))

this.p<-rowMeans( y/ outer(rep(1,nrow(y)),d$lib.size) )
d1p<-logLikDerP(this.p,y,d$lib.size,r=1.5,der=1)

[Package edgeR version 1.0.4 Index]