simCE: CE Simulator

Description

Simulates the capillary elechtrophoresis (CE) process.

Usage

simCE(data, vol = 1, sd.vol = 0, intercept = -7.7662, slope = 0.859,
  sigma = 0.5798, t.intercept = 10.82719, t.slope = 0.9047,
  t.sigma = 0.5951, debug = FALSE)

Arguments

data

data.frame with simulated data. Preferably output from simPCR. Required columns are 'PCR.Vol' and 'PCR.Amplicon'.

vol

numeric for the aliquot PCR product for CE analysis.

sd.vol

numeric for the standard deviation of vol.

intercept

numeric for the intercept of the linear model to scale molecules -> rfu.

slope

numeric for the slope of the linear model to scale molecules -> rfu.

sigma

numeric for the residual standard error of the linear model to scale molecules -> rfu. NB! NOT USED!

t.intercept

numeric for the intercept of the linear model to calculate detection threshold (molecules).

t.slope

numeric for the slope of the linear model to calculate detection threshold (molecules). NB! NOT USED!

t.sigma

numeric for the residual standard error of the linear model to calculate detection threshold (molecules).

debug

logical for printing debug information.

Value

data.frame with simulation results in columns 'CE.xxx'.

Details

Simulates the forensic capillary electrophoresis analysis of PCR product.

Examples

Run this code

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

# Simulate profile.
res <- simProfile(data=df, sim=5, name="Test")

# Simulate sample
res <- simSample(data=res, cells=58, sd.cells=0)

# Simulate extraction.
res <- simExtraction(data=res, vol.ex=1, sd.vol=0, prob.ex=1, sd.prob=0)

# Simulate PCR.
res <- simPCR(data=res, kit=NULL, pcr.cyc=30, vol.aliq=1, sd.vol.aliq=0, vol.pcr=25, sd.vol.pcr=0)

# Simulate CE.
res <- simCE(data=res, vol=1, sd.vol=0, intercept=-10.48, slope=0.86, sigma=0.58)
print(res)