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Simple simulation function

SimpleSim.Rd

Simple simulation function

Usage

SimpleSim(
  nreads = 1000,
  fn = 0.5,
  pnew = 0.05,
  pold = 0.001,
  rlen = 100,
  Ucont = 0.25
)

Arguments

nreads

Number of reads to simulate

fn

Fraction of reads that are new in simulation. Whether a read will be new will be determined by a draw from a Bernoulli(fn) distribution.

pnew

T-to-C mutation rate in new reads

pold

T-to-C mutation rate in old reads

rlen

Length of simulated reads

Ucont

Fraction of nucleotides in simulated reads that are Ts (U in RNA)