tau2.0.objective {edgeR}R Documentation

Objective function for tau2

Description

Objective function for tau2 which is used in the rule of how much to squeeze the dispersion parameters towards the common value

Usage

 
tau2.0.objective(tau2.0, info.g, score.g) 

Arguments

tau2.0 scalar, value for tau2
info.g observed information for each gene
score.g observed score (first derivative of log-likelihood) for each gene

Value

scalar, value of objective function at tau2.0

Author(s)

Mark Robinson

Examples

y<-matrix(rnbinom(20,size=1,mu=10),nrow=5)
x<-list(data=y,group=rep(1:2,each=2),lib.size=rep(1000:1001,each=2))
scores <- condLogLikDerDelta(y, delta=0.5, der = 1, doSum = TRUE) 
qA <- quantileAdjust(x, alpha = 10, null.hypothesis = TRUE)
exp.inf <- approx.expected.info(x, d=0.5, qA)
sigma2.0.est <- optimize(tau2.0.objective, c(0, 500), info.g = exp.inf, score.g = scores)$min

[Package edgeR version 1.0.4 Index]