simSample: Forensic Sample Simulator
In OskarHansson/pcrsim: Simulation of the Forensic DNA Process

Description Usage Arguments Details Value See Also Examples

Simulates the DNA content in forensic stain.

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
)

`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.

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).

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

simProfile

# 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)