findPCRprob: Find PCR probabilities

Description

findPCRprob Find values for the PCR efficiency parameter for simPCR that satisfy the target locus balances.

Usage

findPCRprob(sim, targetLb, acceptedDev = 0.01,
    stepSize = 0.001, seed = 0.75, maxPCRprob = 0.95,
    progress = FALSE, ...)

Arguments

sim

integer for number of simulations.

targetLb

numeric vector with target interlocus balances.

acceptedDev

numeric, accepted deviation from target.

stepSize

numeric, probPCR is changed by this value.

seed

numeric, start value for optimisation of probPCR.

maxPCRprob

numeric, maximal value for optimised PCR efficiency.

progress

logical, print progress to console.

...

arguments to be passed to simPCR

Value

data.frame with additional columns 'N' and 'Mean'.

Details

The interlocus balance for a kit should be characterised during the internal validation of the kit. This function search for PCR efficiency parameters that upon PCR simulation result in similar locus balances.

Examples

Run this code

# Experimental inter locus balances for the STR kit one wants to simulate.
target <- c(0.05,0.05,0.06,0.04,0.04,
             0.04,0.06,0.05,0.05,
             0.04,0.04,0.05,0.05,
             0.15,0.07,0.09,0.07)

# Find PCR efficiency values that upon simulation
# satisfy the experimental data for 0.5 ng of input DNA.
set.seed(10) # For reproducibility.
findPCRprob(sim=40, targetLb=target, ncells=83, progress=FALSE)

# The PCR efficency parameters can now be plugged into the PCR simulation model.