Allow precomputed baseline for single sample pipeline

[wudustan]

For pipelineCNA() a synthetic baseline is calculated per-sample. This can be an issue when you have a large dataset and have to run single samples for computational reasons as the baseline is different for each sample. There should ideally be a way to generate a baseline for whole dataset and then allow that as the subtraction for each sample separately.

Relevant code:

if (length(norm_cell_names) < 1) {
    print("7) Measuring baselines (pure tumor - synthetic normal cells)")
    count_mtx_relat <- removeSyntheticBaseline(count_mtx, par_cores = par_cores)
  } else {
    print("7) Measuring baselines (confident normal cells)")
    if (length(norm_cell_names) == 1) {
      basel <- count_mtx[, which(colnames(count_mtx) %in% norm_cell_names)]
    }
    else {
      basel <- apply(count_mtx[, which(colnames(count_mtx) %in% norm_cell_names)], 1, median)
    }
    count_mtx_relat <- count_mtx - basel
  }