DNAmixture {DNAmixturesLite}

Create a DNA mixture model

Description

A model object for analysis of one or more DNA mixtures. For a brief overview of the package functionality, see in particular DNAmixtures.

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

DNAmixture(
  data,
  k,
  C,
  database,
  K = character(0),
  reference.profiles = NULL,
  dir = character(0),
  domainnamelist = NULL,
  load = FALSE,
  write = FALSE,
  dyes = NULL,
  triangulate = TRUE,
  compile = TRUE,
  compress = TRUE,
  use.order = TRUE
)

## S3 method for class 'DNAmixture'
print(x, ...)

Arguments

data

A list containing one data.frame for each DNA mixture. Note, that in the special case of analysing just one mixture, this still has to be specified as list(data). Each dataset should contain variables marker, allele, and frequency. Optionally, also a column for each reference profile specified in K.

k

Number of contributors.

C

A list of thresholds, one for each mixture.

database

A data.frame containing at least variables marker, allele, frequency.

K

Names of reference profiles; these can be chosen freely, but should match (possibly only a subset of) the names specified by the reference profiles.

reference.profiles

A data.frame containing allele counts for each reference profile, if not specified in data.

dir

Location of network files if loading or saving the networks.

domainnamelist

Names of marker-wise network files (without hkb-extension). Default is the set of markers.

load

Read networks from disk?

write

Save networks as hkb files?

dyes

A list containing a list of dyes indexed by markers

triangulate

Triangulate the networks? Default is to triangulate the network using a good elimination order.

compile

Compile the networks?

compress

Compress the network? Defaults to TRUE and is strongly recommended for models with a large number of contributors.

use.order

Should the default elimination order be used for triangulation? Otherwise the "total.weight" heuristic for triangulation in Hugin is used.

x

An object of class DNAmixture.

...

not used.

Details

The names for known contributors can be chosen freely, whereas unknown contributors are always termed U1,U2, ....

We allow for stutter to an allele one repeat number shorter. The range of alleles at a marker is defined by the union of alleles specified though the peak heights, the reference profiles, and the allele frequencies. Any alleles that are included, but not found in the database, will be assigned frequency NA, and it is then up to the user to decide on further actions. If a particular mixture has no observations at a marker, the heights are set to NA, but if the mixture has some peaks at that marker, then missing heights are all set to 0. Note that we hereby cover the possibility that mixtures are analysed with different kits, and so are observed at different markers. We do not (readily) allow kits to have different ranges of possible alleles at one marker.

If amelogenin is included in the analysis, the marker should be named "AMEL" and an integer coding such as X=0, Y=1, where X is assigned a lower number than Y, should be used. Note that in terms of amelogenin, the allele frequencies have a slighly different interpretation to that for other markers, in that they denote the probability of having an additional X or Y to the X that all people have. Thus, a natural choice will be p(X)=p(Y)=0.5, denoting equal probability of a male or female contributor.

Value

An object of class DNAmixture. This contains amongst other things

markers

The joint set of markers used for the mixtures specified.

domains

For models involving unknown contributors, a list containing one Bayesian network (hugin.domain) per marker; see buildMixtureDomains for details on the networks

data

A list containing for each marker the combined allele frequencies, peak heights, and reference profiles as produced by DNAmixtureData.

Examples

data(MC15, MC18, USCaucasian)
DNAmixture(list(MC15, MC18), C = list(50,50), k = 3, K = c("K1", "K2"),
           database = USCaucasian)
DNAmixture(list(MC15, MC18), C = list(50,50), k = 3, K = c("K3", "K1", "K2"),
           database = USCaucasian)