simDilution: Serial Dilution Simulator

Description Usage Arguments Details Value Examples

View source: R/simDilution.r

Description

Simulates the serial dilution process of a DNA extract.

Usage

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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

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# 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)

pcrsim documentation built on May 29, 2017, 3:53 p.m.