R/methods-ff_array.R

In MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

## Fix strange behavor for [ with ff_arrays.

#' @aliases "[",ff_array,ANY-method
#' @rdname TrioSet-class
setMethod("[", signature(x="ff_array"), function(x, i, j, ..., drop=FALSE){
  if(missing(drop)) drop <- TRUE
  if(length(list(...)) > 0){
    k <- list(...)[[1]]
    if(is(k, "character")) {
      k <- match(dimnames(x)[[3]])
      stopifnot(length(k)>0)
    }
  } else k <- NULL
  if(is.null(k)){
    if(!missing(i) & missing(j)){
      x <- x[i, 1:ncol(x), 1:3, ..., drop=drop]
    }
    if(!missing(i) & !missing(j)){
      x <- x[1:nrow(x), j, 1:3, drop=drop]
    }
    if(missing(i) & !missing(j)){
      x <- x[1:nrow(x), j, 1:3, drop=drop]
    }
  } else {
    if(!missing(i) & missing(j)){
      x <- x[i, 1:ncol(x), k, drop=drop]
    }
    if(!missing(i) & !missing(j)){
      x <- x[i, j, k, drop=drop]
    }
    if(missing(i) & !missing(j)){
      x <- x[1:nrow(x), j, k, drop=drop]
    }
  }
  return(x)
})