calibrateLb: Calibrate Inter-locus Balance
In OskarHansson/pcrsim: Simulation of the Forensic DNA Process

Description Usage Arguments Details Value Examples

Estimate values for the PCR efficiency parameter per locus that satisfy the target inter-locus balances.

calibrateLb(
  sim = 100,
  target,
  amount = 0.5,
  cell.dna = 0.006,
  pcr.cyc = 30,
  acc.dev = 0.001,
  step.size = 0.001,
  seed = 0.85,
  max.eff = 0.98,
  progress = TRUE,
  debug = FALSE
)

`sim`	integer the number of simulations per calibration cycle.
`target`	numeric vector with target interlocus balances.
`amount`	numeric for amount of DNA in ng.
`cell.dna`	numeric the DNA content of a diploid cell in nanograms (default is 0.006 ng).
`pcr.cyc`	integer the number of PCR cycles.
`acc.dev`	numeric, accepted deviation from target.
`step.size`	numeric, the probability of PCR is changed by this value.
`seed`	numeric, start value for optimisation of the PCR probability.
`max.eff`	numeric, maximal value for estimated PCR efficiency.
`progress`	logical, print progress to console.
`debug`	logical to print debug information.

The inter-locus balance for a kit should be characterised during the internal validation of the kit. The function search for PCR efficiency values per locus that upon simulation are similar to the target inter-locus balances. Use the PCR efficiency value obtained from the calibratePCRsim function as seed value.

vector with estimated PCR efficiencies for each locus.

# Experimental inter-locus balances for the STR kit to be simulated (sums to 1).
target <- c(0.20, 0.10, 0.15, 0.25, 0.30)
 
# Find PCR efficiency values that upon simulation
# satisfy the experimental data for 0.5 ng of input DNA.
set.seed(10) # For reproducibility.
calibrateLb(sim=10, target=target, amount=0.5, seed=0.85, progress=FALSE)

# Locus specific PCR efficency parameters can now be used as parameters.
# [1] 0.858 0.816 0.841 0.871 0.883