pcrsim (version 0.1.1)

simulateProfile: Simulate DNA profiles

Description

simulateProfile simulates entire DNA profiles.

Usage

simulateProfile(alleles, sample.name = NULL, ncells = NA,
    ncells.sd = 0, conc = NA, conc.sd = 0, intercept = NA,
    intercept.sd = 0, slope = NA, slope.sd = 0,
    exprob = NA, exprob.sd = 0, volume = NA, volume.sd = 0,
    aliq = NA, aliq.sd = 0, simulations = 1, kit = NA,
    celldna = 0.006, ...)

Arguments

alleles

list of alleles per marker.

sample.name

character string giving optional sample name.

ncells

numeric, number of cells ( = number of DNA molecules of each allele).

ncells.sd

numeric, standard deviation.

conc

numeric, human DNA concentration in DNA extract.

conc.sd

numeric, standard deviation.

intercept

numeric, degradation intercept.

intercept.sd

numeric, standard deviation for degradation intercept.

slope

numeric, degradation slope.

slope.sd

numeric, standard deviation for degradation slope.

exprob

numeric [0-1], probability that an allele survivives the extraction (extraction efficiency).

exprob.sd

numeric, standard deviation for the extraction efficiency.

volume,

numeric, final extraction volume.

volume.sd,

numeric, standard deviation for the final extraction volume.

aliq

numeric, volume of DNA extract taken for PCR amplification.

aliq.sd

numeric, standard deviation for volume of DNA extract.

kit

string or integer specifying an STR typing kit.

simulations

integer, number of simulations.

celldna,

numeric giving the DNA content of a cell.

...

arguments to be passed to simPCR

Value

• list with simulation results.

Details

Simulates the peak heights for a single person profile. Integration of degradation and interlocus balance. Handle missing alleles. Only single person profiles, unique(alleles) will be applied.

Examples

# Define a DNA profile.
dnaProfile <- list(c("X","Y"),c(17,18),c(6,9.3),c(29,31.2),c(16,18),
c(13,15),c(12,13),c(22,25),c(9,13),
c(16,16),c(16,19),c(14,15),c(20,23),
c(10,14),c(18,23),c(13,14),c(15,16))

# Simulate.
simulateProfile(alleles=dnaProfile, kit="ESX17", simulations=5,
 ncells=200, ncells.sd=20,
 exprob=0.7, exprob.sd=0.1,
 volume=200, volume.sd=20,
 aliq=17.5, aliq.sd=1)