simDilution: Serial Dilution Simulator

In pcrsim: Simulation of the Forensic DNA Process

Description

Simulates the serial dilution process of a DNA extract.

Usage

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)

Arguments

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.

Details

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).

Value

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.

Examples

# 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)

Example output

Loading required package: strvalidator
R session is headless; GTK+ not initialized.
STR-validator 2.0.0 loaded!
PCRsim 1.0.2 loaded!
SIMULATE PROFILE
'Sim' column added.
'Sample.Name' column added.
SIMULATE SAMPLE
'Sample.Haploid' column added.
'Sample.Cells' column added.
'DNA' column added.
SIMULATE EXTRACTION
'Ex.Vol' column added.
'Ex.Prob' column added.
'Ex.DNA' column added.
'Ex.Conc' column added.
'Volume' column added.
'DNA' column updated!
Fixed number of dilutions (3). Target amount in PCR:
0.5, 0.25, 0.125
SIMULATE DILUTION
'Dil.DNA.Pre' column added.
'Dil.Prob' column added.
'Dil.Vol.Ser' column added.
'Dil.DNA.Ser' column added.
'Dil.Vol' column added.
'Dil.DNA' column added.
'Dil.Conc' column added.
'Volume' column updated!
'DNA' column updated!

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