pcrsim (version 1.0.1)

calibrateLb: Calibrate Inter-locus Balance

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.

Value

vector with estimated PCR efficiencies for each locus.

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.

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