simDegradation: DNA Degradation Simulator
In OskarHansson/pcrsim: Simulation of the Forensic DNA Process

Description Usage Arguments Details Value See Also Examples

Simulates the degradation of DNA.

1	simDegradation(data, kit, deg, quant.target, debug = FALSE)

`data`	data.frame with simulated data. Preferably output from `simSample`. Required columns are 'Allele', 'DNA', and 'Sim'.
`kit`	character string for STR DNA amplification kit.
`deg`	numeric for the estimated degradation probability (chance per base pair)
`quant.target`	integer defining the quantification target size in base pair.
`debug`	logical TRUE to indicate debug mode.

Simulates the DNA degradation process by calculating the probability that a DNA fragment of the specific size (bp) is complete i.e. not degraded. Then a binomial selection of non-degraded molecules takes place with the previously calculated probability. The number of molecules is taken from the required column 'DNA' which is floored to avoid NAs in the rbinom function.

data.frame with simulated results in columns 'Deg.Par', 'Deg.Prob', and 'Deg.DNA'.

simSample

# Simulate profile.
# Get allele frequency database.
require(strvalidator)
db <- strvalidator::getDb(getDb()[2])
# Simulate profile.
res <- simProfile(kit= "ESX17", db=db, sim=10, name="Test")
# Simulate sample.
res <- simSample(data=res, cells=5000)
# Simulate degradation.
res <- simDegradation(data=res, kit="ESX17", deg=0.03, quant.target=80)
print(res)