R/check_contrasts.R

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

#' Check contrasts
#'
#' Check all possible contrasts used by \code{\link{results_all}}.  Following
#' DESeq2 conventions, control group should be listed first and then pairswise
#' comparisons are selected in reverse order, so A, B, C levels will return
#' C vs. B, C vs. A, and B vs. A
#'
#' @param trt a vector
#' @param vs either compare all vs. all (default) or a all vs. a specific treatment, or see note.
#'
#' @note If you combine factors of interest into a single group following section 3.3 in the DESeq2 vignette,
#'  you can set vs = "combined" to limit the comparisons to those within the first group.
#'
#' @return A vector of contrasts
#'
#' @author Chris Stubben
#'
#' @examples
#'  # check_contrasts(samples$trt)
#'  trt <- c("B", "A", "C")
#'  # sorted alphabetically and then reverse order combn
#'  check_contrasts(trt)
#'  # or specify factor levels with control first
#'  check_contrasts(factor(trt, levels = c("C", "B", "A")))
#'  # combine 2 trt groups  (66 possible contrasts)
#'  trt <- paste( 1:4, rep(c("A", "B", "C"), each=4))
#'  check_contrasts( trt, vs = "combined")
#' @export

check_contrasts <- function(trt, vs="all"){
   if(is.factor(trt)){
      n <- levels( trt )
   }else{
	   # DESeq2 will create factor for character strings in alphabetical order
      n <- sort(unique(trt))
   }
   contrast <- utils::combn(n, 2)[2:1,, drop=FALSE]
   if( vs == "combined"){
      ## if two columns are combined into a single trt group, compare within first group
      n1 <- apply(contrast, 2, function(x) length(unique( gsub("[ _-].+", "", x)))==1)
      contrast <- contrast[, n1]
   }else if( vs %in% n){
      contrast <- rbind( vs, n[n!=vs])
   }
   vs <- apply(contrast, 2, paste, collapse = " vs. ")
   message(length(vs), " contrasts: ")
   vs
}