Make a matrix indicating which samples are replicates.

RUVSeq_makeGroups.R

#' Make a matrix suitable for use with RUVSeq methods such as RUVs().
#' 
#' Each row in the returned matrix corresponds to a set of replicate samples.
#' The number of columns is the size of the largest set of replicates; rows for
#' smaller sets are padded with -1 values.
#' 
#' @param xs A vector indicating membership in a group.
#' @seealso RUVSeq::RUVs
#' @example 
#'  makeGroups(c("A","B","B","C","C","D","D","D","A"))
#'       [,1] [,2] [,3]
#'  [1,]    1    9   -1
#'  [2,]    2    3   -1
#'  [3,]    4    5   -1
#'  [4,]    6    7    8
makeGroups <- function(xs) {
  xs <- factor(xs)
  groups <- matrix(-1, nrow = length(levels(xs)), ncol = max(table(xs)))
  for (i in 1:length(levels(xs))) {
    idxs <- which(xs == levels(xs)[i])
    groups[i,1:length(idxs)] <- idxs
  }
  groups
}