simDilution: Serial Dilution Simulator
In OskarHansson/pcrsim: Simulation of the Forensic DNA Process

Description Usage Arguments Details Value Examples

Simulates the serial dilution process of a DNA extract.

simDilution(
  data = NULL,
  stock.conc = 10,
  stock.vol = 1000,
  stock.aliq = 5,
  amount = c(1, 0.1),
  steps = 3,
  dilution.factor = 0.5,
  dilution.aliq = 100,
  pcr.aliq = 17.5,
  cell.dna = 0.006,
  truncate.top = TRUE,
  debug = FALSE
)

`data`	data.frame with simulated data.
`stock.conc`	numeric for the stock concentration (ng/ul).
`stock.vol`	numeric for the stock volume (ul).
`stock.aliq`	numeric for the aliquot volume pipetted from the stock solution (ul).
`amount`	numeric for the highest target amount in the PCR reaction (ng) or a vector of length two giving the target range c(high, low).
`steps`	numeric for the number of dilution steps.
`dilution.factor`	numeric between 0 and 1 for the dilution factor (i.e. 0.5 for a two-fold dilution).
`dilution.aliq`	numeric for the aliquot pipetted in each serial dilution step (excluding from stock solution).
`pcr.aliq`	numeric for the aliquot forwarded to PCR (ul).
`cell.dna`	numeric to indicate the DNA content of a diploid cell in nanograms (ng).
`truncate.top`	logic if TRUE the high concentrations will be discarded if there are too few simulated samples in 'data'. If FALSE the low concentrations will be discarded.
`debug`	logical flagging for debug mode.

Simulates the dilution process by binomial selection of molecules from a stock of extracted DNA. Result include columns with number of molecules prior to the binomial selection (Dil.DNA.Pre) the probability used (Dil.Prob), the total volume of each serial dilution prior to removal of aliquot for the subsequent dilution (Dil.Vol.Ser), the number of molecules in each serial dilution prior to removal of aliquot for the subsequent dilution (Dil.DNA.Ser), final volume after serial dilution is complete (Dil.Vol), final number of molecules after serial dilution is complete (Dil.DNA), and target concentration used in calculations (Dil.Conc).

data.frame with simulation results in columns 'Dil.DNA.Pre', 'Dil.Prob', 'Dil.Vol.Ser', 'Dil.DNA.Ser', 'Dil.Vol', 'Dil.DNA', and 'Dil.Conc'. Columns 'Volume' and 'DNA' are added or updated to be used subsequently.

# Create a data frame with a DNA profile.
markers = rep(c("D3S1358","TH01","FGA"), each=2)
alleles = c(15,18,6,10,25,25)
res <- data.frame(Marker=markers, Allele=alleles)

# Simulate profile.
res <- simProfile(data=res, sim=3, name="Test")

# Simulate diploid sample.
res <- simSample(data=res, cells=10000, sd.cells=200)

# Simulate extraction.
res <- simExtraction(data=res, vol.ex=200, sd.vol=10, prob.ex=0.3, sd.prob=0.1)

# Simulate dilution.
res <- simDilution(data=res, amount=1, dilution.factor=0.5)