Vectorized simulation of one replicate of multi-label NR-seq data

Generalizes SimulateOneRep() to simulate any combination of mutation types. Currently, no kinetic model is used to relate certain parameters to the fractions of reads belonging to each simulated mutational population. Instead these fractions are drawn from a Dirichlet distribution with gene-specific parameters.

Usage

VectSimulateMultiLabel(
  nfeatures,
  populations = c("TC"),
  fraction_design = create_fraction_design(populations),
  fractions_matrix = NULL,
  read_vect = NULL,
  sample_name = "sampleA",
  feature_prefix = "Gene",
  kdeg_vect = NULL,
  ksyn_vect = NULL,
  logkdeg_mean = -1.9,
  logkdeg_sd = 0.7,
  logksyn_mean = 2.3,
  logksyn_sd = 0.7,
  phighs = stats::setNames(rep(0.05, times = length(populations)), populations),
  plows = stats::setNames(rep(0.002, times = length(populations)), populations),
  seqdepth = nfeatures * 2500,
  readlength = 200,
  alpha_min = 3,
  alpha_max = 6,
  Ucont = 0.25,
  Acont = 0.25,
  Gcont = 0.25,
  Ccont = 0.25
)