Merge a list of data.tables

mergeDT.R

# Could be generalised to handle the full arguments of merge.data.table but I've kept it simple.
# mergeDT based on http://r.789695.n4.nabble.com/merge-multiple-data-frames-td4331089.html
# Takes a (named) list of data.tables (lodt) where all columns are common to all data.tables
# The key of each table is the same but is only a subset of the columns, e.g. (chr, pos1, pos2)
# The remaining columns of each data.table are the "counts", e.g. (MM, MU, UM, UU)
# We append the names of each sample (the names of lodt) to the "counts" so that we can keep 
# track of from which sample the counts came.
mergeAll <- function(lodt) { 
  dotNames <- lapply(lodt, names)
  repNames <- Reduce(intersect, dotNames)
  repNames <- repNames[repNames != key(lodt[[1]])]
  for(i in seq_along(lodt)){ 
    wn <- which((names(lodt[[i]]) %in% repNames) & 
                  (names(lodt[[i]]) != key(lodt[[1]])))
    setnames(lodt[[i]], wn, 
             paste(names(lodt[[i]])[wn], names(lodt)[[i]], sep = "."))
  }
  Reduce(function(x, y) merge(x, y, all = TRUE), lodt)
}