calibrateLb: Calibrate Inter-locus Balance

In pcrsim: Simulation of the Forensic DNA Process

Description

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

Usage

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)

Arguments

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.

Details

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.

Value

vector with estimated PCR efficiencies for each locus.

Examples

# 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 

pcrsim documentation built on May 2, 2019, 2:40 a.m.