designAsFactor <- function(design)
#	Construct a factor from the unique rows of a matrix
#	Gordon Smyth
#	11 March 2011.  Last modified 19 March 2011.
{
	design <- as.matrix(design)
	z <- (exp(1)+pi)/5
	g <- factor(rowMeans(design*z^(col(design)-1)))
	levels(g) <- 1:length(levels(g))
	g
}

mglmOneWay <- function(y,design=NULL,dispersion=0,offset=0,weights=NULL,maxit=50,tol=1e-10,coef.start=NULL)
#	Fit multiple negative binomial glms with log link
#	by Fisher scoring with
#	only a single explanatory factor in the model
#	Gordon Smyth
#	11 March 2011.  Last modified 11 Sep 2014.
{
	y <- as.matrix(y)
	ntags <- nrow(y)
	nlibs <- ncol(y)
	if(is.null(design)) {
		design <- matrix(1,nlibs,1)
		group <- factor(design)
	} else {
		design <- as.matrix(design)
		group <- designAsFactor(design)
	}
	ngroups <- length(levels(group))
	stopifnot(ncol(design)==ngroups)
	mu <- matrix(0,ntags,ngroups)
	offset <- expandAsMatrix(offset,dim(y))
	if(!is.null(weights)) weights <- expandAsMatrix(weights,dim(y))
	
	firstjofgroup <- rep(0,ngroups)
	new.start <- NULL
	for (g in 1:ngroups) {
		j <- which(group==(levels(group)[g]))
		firstjofgroup[g] <- j[1]
		if (!is.null(coef.start)) { new.start <- coef.start %*% design[firstjofgroup[g],] }
		mu[,g] <- mglmOneGroup(y[,j,drop=FALSE],dispersion=dispersion,offset=offset[,j,drop=FALSE],weights=weights[,j,drop=FALSE],maxit=maxit,tol=tol,
			coef.start=new.start)
	}

	designunique <- design[firstjofgroup,,drop=FALSE]
	mu1 <- pmax(mu,-1e8)
	beta <- t(solve(designunique,t(mu1)))
	mu <- mu[,group,drop=FALSE]
	mu <- exp(mu+offset)
	list(coefficients=beta,fitted.values=mu)
}
