snv-benchmark.R

snv-benchmark.R

snv_impl_base <- function(X) {
  X <- as.matrix(X)
  X <- sweep(X, 1L, rowMeans(X, na.rm = TRUE), `-`)
  X_sc <- sweep(X, 1L, apply(X, 1L, sd, na.rm = TRUE), `/`)
  return(X_sc)
}

snv_impl_base_mstats <- function(X) {
  X <- as.matrix(X)
  X <- sweep(X, 1L, matrixStats::rowMeans2(X, na.rm = TRUE), `-`)
  X_sc <- sweep(X, 1L, matrixStats::rowSds(X, na.rm = TRUE), "/")
  return(X_sc)
}

snv_impl_dt <- function(X) {
  X[, colnames(X) :=
    lapply(.SD, function(x) x - rowMeans(as.matrix(x), na.rm = TRUE)),
  .SDcols = colnames(X)
  ]
  X[, colnames(X) :=
    lapply(.SD, function(x) x - sd(x, na.rm = TRUE)),
  .SDcols = colnames(X)
  ]
  X <- as.matrix(X)
  return(X)
}