rPeakHeight {DNAmixturesLite}

Simulate peak heights from a DNA mixture model.

Description

A set of peak heights is sampled for each mixture in the model. Note that if the mixtures cover different sets of markers, so will the simulated peak heights. If there are unknown contributors, their genotypes are sampled from the networks in mixture$domains, but these genotypes are not stored.

IMPORTANT: This is the DNAmixturesLite package, which is intended as a service to enable users to try DNAmixtures without purchasing a commercial licence for Hugin. When at all possible, we strongly recommend the use of DNAmixtures rather than this lite-version. See https://dnamixtures.r-forge.r-project.org/ for details on both packages.

While the lite-version seeks to provide the full functionality of DNAmixtures, note that computations are much less efficient and that there are some differences in available functionality. Be aware that the present documentation is copied from DNAmixtures and thus may not accurately describe the implementation of this lite-version.

Usage

rPeakHeight(
  mixture,
  pars,
  nsim = 1,
  markers = mixture$markers,
  dist = c("joint", "conditional"),
  use.threshold = TRUE,
  initialize = TRUE,
  ...
)

Arguments

mixture

A DNAmixture.

pars

A mixpar model parameter.

nsim

Number of simulations for each allele.

markers

Subset of markers to simulate

dist

How should observed peak heights be taken into account? Possible choices are

"joint"

which does not take peak heights into account.

"conditional"

which takes all peak heights into account, except that for the peak under consideration.

use.threshold

Should peak heights under the detection threshold C be set to 0? Defaults to TRUE, corresponding to simulating under the model fitted.

initialize

Should all propagated evidence be removed from the network? Defaults to TRUE. If set to FALSE, the user should make sure to check whether the networks represent the distribution of interest.

...

Not used.

Value

A list of one three-way array per marker; the three margins correspond to traces, alleles, and simulations.

Author(s)

Therese Graversen

Examples

data(MC15, MC18, USCaucasian)

mixP <- DNAmixture(list(MC15, MC18), C = list(50, 38), k = 3, K = c("K1", "K3", "K2"),
                   database = USCaucasian)
pP <- mixpar(rho = list(30, 30), eta = list(30, 30), xi = list(0.08, 0.08),
             phi = list(c(K2 = 0.1, K3 = 0.2, K1 = 0.7), c(K2 = 0.1, K3 = 0.2, K1 = 0.7)))
rpk <- rPeakHeight(mixP, pP, nsim = 5)


mixD <- DNAmixture(list(MC15, MC18), C = list(50, 38), k = 3, K = c("K1", "K3"),
                   database = USCaucasian)
pD <- mixpar(rho = list(30, 30), eta = list(30, 30), xi = list(0.08, 0.08),
             phi = list(c(U1 = 0.1, K3 = 0.2, K1 = 0.7), c(U1 = 0.1, K3 = 0.2, K1 = 0.7)))
rpj <- rPeakHeight(mixD, pD, nsim = 5, dist = "joint")
rpc <- rPeakHeight(mixD, pD, nsim = 5, dist = "conditional")