DNAmixtureData {DNAmixturesLite}

Create a data set for a DNA mixture model

Description

The function is intended for internal use in DNAmixture and its purpose is to combine peak height data, any reference profiles, and allele frequencies.

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

DNAmixtureData(data, database, K = character(0), reference.profiles = NULL)

Arguments

data

Either one data.frame containing variables markers and allele, height, or a list of one or more of such data.frames, corresponding to each EPG. If a data.frame with reference profiles are not specified separately, these should be found amongst the datasets.

database

A data.frame with variables marker, allele, and allele frequency.

K

Names for reference profiles.

reference.profiles

Optionally, a data.frame containing allele counts for each reference profile specified in K. There should be one variable for each name in K as well as variables marker and allele.

Value

list of data.frame's indexed by markers and containing variables

marker

The STR marker

allele

Repeat number of the allele

frequency

Allele frequency

height1, ..., heightN

Peak heights for each of the N mixtures analysed; their order follows the order in which the mixtures are specified in data.

stutter.from

For internal use. Where do the alleles get stutter from? A value of -1 means that the allele cannot receive stutter, corresponding to gets_stutter being false. allele[i] receives stutter from allele[stutter.from[i]]

stutter.to

As above. allele[i] can stutter to allele[stutter.to[i]]

as well as known DNA profiles as labelled by K.

Author(s)

Therese Graversen

Examples

## Create a dataset for two markers with each 3 observed alleles
epgdf <- data.frame(marker = rep(c("FGA", "TH01"), each = 3),
                    allele = c(18, 23, 27, 7, 8, 9.3), ## Observed alleles
                    height = c(100, 100, 200, 200, 100, 100), ## Peak heights
                    Anna = c(0,0,2,1,0,1),             ## Anna's profile
                    Peter = c(1,1,0,1,1,0))            ## Peter's profile

data(USCaucasian)
dat <- DNAmixtureData(epgdf, K = c("Anna", "Peter"), database = USCaucasian)