pcrsim (version 1.0.2)

simSample: Forensic Sample Simulator

Description

Simulates the DNA content in forensic stain.

Usage

simSample(data, cells = NULL, sd.cells = 0, conc = NULL, sd.conc = 0,
  vol = NULL, sd.vol = 0, cell.dna = 0.006, haploid = FALSE,
  kit = NULL, slope = NULL, intercept = NULL, debug = FALSE)

Arguments

data

data.frame with columns 'Marker', 'Allele', and 'Sim' defining the DNA profiles and simulation id (counter). Preferably output from simProfile.

cells

integer for the estimated number of cells.

sd.cells

numeric for the standard deviation of cells.

conc

numeric for the estimated DNA concentration.

sd.conc

numeric for the standard deviation of conc.

vol

numeric for the estimated sample volume.

sd.vol

numeric for the standard deviation of vol.

cell.dna

numeric to indicate the DNA content of a diploid cell in nanograms (ng).

haploid

logical TRUE to indicate haploid cells.

kit

character string defining the DNA typing kit used to calculate allele size (used to calculate allele sizes needed for the regression option i.e. slope and intercept).

slope

numeric from regression of log concentration by fragment size (bp).

intercept

numeric from regression of log concentration by fragment size (bp).

debug

logical TRUE to indicate debug mode.

Value

data.frame with simulated result in columns 'Cells'.

Details

Simulates the number of DNA molecules in a forensic stain either from: 1) An estimate of the number of cells in the stain. 2) The DNA concentration. 3) The slope and intercept values as obtained from log-linear regression of DNA concentration by size in basepair. The regression emulates degradation and should not be used together with simulation of degradation using simDegradation. Some parameters accept vectors so that simulated samples can have different number of cells and be a mixture of haploid and diploid samples (see examples). Note 1: Number of cells can be decimal values since it is an estimate. Note 2: Number of cells will always be integer if haploid=TRUE because binomial selection require integer values. Note 3: To get the same total amount of DNA in samples with diploid and haploid cells. the parameter for haploid cells must be: cells = 2 * number_of_diploid_cells NB! Important that each marker has two rows (i.e. homozygotes is e.g. 16, 16).

See Also

simProfile

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)
df <- data.frame(Marker=markers, Allele=alleles)
# Simulate profile.
prof <- simProfile(data=df, sim=3, name="Test")

# Simulate diploid sample.
res <- simSample(data=prof, cells=100, sd.cells=20)
print(res)

# Simulate haploid sample.
res <- simSample(data=prof, cells=100, sd.cells=20, haploid=TRUE)
print(res)

# Simulate haploid sample from concentration.
res <- simSample(data=prof, conc=0.02, sd.conc=0.001, vol=100, haploid=TRUE)
print(res)

# Simulate sample from slope and intercept.
res <- simSample(data=prof, vol=100, slope=-0.01, intercept=0.20, kit="SGMPlus")
print(res)

# Simulate mixture of diploid and haploid sample types of two concentrations.
res <- simSample(data=prof, cells=c(1000,1000,250), haploid=c(FALSE,TRUE,FALSE))
print(res)