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simDNAmixtures (version 1.0.1)

Simulate Forensic DNA Mixtures

Description

Mixed DNA profiles can be sampled according to models for probabilistic genotyping. Peak height variability is modelled using a log normal distribution or a gamma distribution. Sample contributors may be related according to a pedigree.

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Install

install.packages('simDNAmixtures')

Monthly Downloads

574

Version

1.0.1

License

GPL (>= 3)

Maintainer

Maarten Kruijver

Last Published

May 4th, 2022

Functions in simDNAmixtures (1.0.1)

allele_specific_stutter_model

Stutter model where the expected stutter rate depends on the allele and locus

Defines a gamma model for peak height variability

read_allele_freqs

Read allele frequencies in FSIgen format (.csv)

SMASH_to_wide_table

Converts SMASH (SampleName, Marker, Allele, Size, Height) data to a wide table

global_stutter_model

Global stutter model where the expected stutter rate is constant across alleles and loci

read_size_regression

Reads a size regression file

Properties such as loci, dye, sizes for most standard forensic kits

read_wide_table

Read wide table (.txt) with Allele1, Allele2, ... columns as is

read_stutter_regression

Reads a stutter regression file

Sample Locus Specific Amplification Efficiency (LSAE) according to prior

sample_log_normal_model

Sample log normal model(s) with parameters according to priors

sample_contributor_genotypes

Sample genotypes for mixture contributors according to allele frequencies

sample_mixtures

Sample mixtures with random genotypes and random parameters according to priors

sample_mixture_from_genotypes

Sample mixture profile with provided genotypes

Defines a stutter type to be used in the allele specific stutter model.

sample_log_normal_stutter_variance

Sample log normal stutter variance parameters according to priors

sample_genotype

Sample a genotype according to allele frequencies

sample_pedigree_genotypes

Sample genotypes for pedigree according to allele frequencies by allele dropping.

sample_offspring

Sample offspring from two parental genotypes

sample_gamma_model

Sample gamma model(s) with parameters according to priors

Stutters and size regressions for a GlobalFiler 3500 kit

read_stutter_exceptions

Reads a stutter exceptions file with overrides for expected stutter ratios

log_normal_model

Defines a log normal model for peak height variability