R/write.R

In richierocks/limma2: Linear Models for Microarray Data

#  OUTPUT

write.fit <- function(fit, results=NULL, file, digits=3, adjust="none", method="separate", F.adjust="none", sep="\t", ...) {
#	Write an MArrayLM fit to a file
#	Gordon Smyth
#	14 Nov 2003.  Last modified 16 June 2008.

	if(!is(fit, "MArrayLM")) stop("fit should be an MArrayLM object")
	if(!is.null(results) && !is(results,"TestResults")) stop("results should be a TestResults object")
	if(is.null(fit$t) || is.null(fit$p.value)) fit <- eBayes(fit)
	method <- match.arg(method, c("separate","global"))

	p.value <- as.matrix(fit$p.value)
	if(adjust=="none") {
		p.value.adj <- NULL
	} else {
		p.value.adj <- p.value
		if(method=="separate") for (j in 1:ncol(p.value)) p.value.adj[,j] <- p.adjust(p.value[,j],method=adjust)
		if(method=="global") p.value.adj <- p.adjust(p.value,method=adjust)
	}
	if(F.adjust=="none" || is.null(fit$F.p.value))
		F.p.value.adj <- NULL
	else
		F.p.value.adj <- p.adjust(fit$F.p.value,method=F.adjust)

	rn <- function(x,digits=digits) if(is.null(x))
		NULL
	else {
		if(is.matrix(x) && ncol(x)==1) x <- x[,1]
		round(x,digits=digits)
	}
	tab <- list()
	tab$A <- rn(fit$Amean,digits=digits-1)
	tab$Coef <- rn(fit$coef,digits=digits)
	tab$t <- rn(fit$t,digits=digits-1)
	tab$p.value <- rn(p.value,digits=digits+2)
	tab$p.value.adj <- rn(p.value.adj,digits=digits+3)
	tab$F <- rn(fit$F,digits=digits-1)
	tab$F.p.value <- rn(fit$F.p.value,digits=digits+2)
	tab$F.p.value.adj <-tab$F.p.value.adj <- rn(F.p.value.adj,digits=digits+3)
	tab$Res <- unclass(results)
	tab$Genes <- fit$genes
	tab <- data.frame(tab,check.names=FALSE)
	write.table(tab,file=file,quote=FALSE,row.names=FALSE,sep=sep,...)
}