R/multiTopTab.R

In jdreyf/ezlimma: Streamlines and extends limma package

#' Combine one or more toptables extracted from linear model fit
#' 
#' Combine one or more toptables extracted from \code{fit} using \code{\link{eztoptab}}.
#' 
#' @inheritParams eztoptab
#' @inheritParams limma_contrasts
#' @seealso \code{\link{eztoptab}}.
#' @return Data frame

multiTopTab <- function(fit, cols=c("P.Value", "adj.P.Val", "logFC"), adjust.method="BH"){
  # remove spaces in names of contrasts to be valid R colnames
  contrasts <- gsub(" ", "", colnames(fit$contrasts))
  # get gene order
  # limma 3.16 has row.names=row number & "ID" column; limma 3.18 has row.names=ID
  # fit doesn't have F-stat if using limma::treat()
  # If coef has single value, then uses moderated t-statistics/p-values
  # If coef is null, then tests all coefs except "(Intercept)"
  if (!is.null(fit$F) & ncol(fit$coefficients) > 1){
    ttf <- limma::topTable(fit, number=Inf)
  } else {
    ttf <- limma::topTable(fit, coef=1, number=Inf, sort.by="p")
  }
  genes <- rownames(ttf)
	# go thru contrasts
	for (i in 1:length(contrasts)){
	  mtt.tmp <- eztoptab(fit, coef=i, cols=cols, adjust.method=adjust.method)
	  # this line alters "" rowname to "NA"
	  mtt.tmp <- mtt.tmp[genes,, drop=FALSE]
	  colnames(mtt.tmp) <- paste(contrasts[i], colnames(mtt.tmp), sep=".")
    if (i==1){
      mtt <- mtt.tmp
    } else {
      mtt <- cbind(mtt, mtt.tmp)
    }
	}
	return(mtt)
}