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DNAprofiles

DNAprofiles is an R-package for studying forensic DNA profiling. In particular, it can be used to study the properties of familial database searching. The main feautures include sampling of DNA profiles/databases as well as relatives of profiles, database comparison exercises, likelihood ratio computations and there are/will be methods to efficiently evaluate the distribution of likelihood ratios. The package is currently work-in-progress and contributions are welcome.

The quickest way to get the development version of the package running locally is using devtools:

require(devtools)
install_github(repo="MaartenKruijver/DNAprofiles")
require(DNAprofiles)

Examples at https://github.com/MaartenKruijver/DNAprofiles_examples

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Version

Install

install.packages('DNAprofiles')

Monthly Downloads

24

Version

0.3.1

License

GPL (>= 2)

Maintainer

Maarten Kruijver

Last Published

April 21st, 2015

Functions in DNAprofiles (0.3.1)

Allelic frequencies at 10 SGMplus loci

find.kth.element

Quickly finds the k'th largest element in a (large) vector

dist.unique.events

Trim probability distribution to unique events with positive probability

Compute exact LR exceedance probabilities

Estimate allelic frequencies in reference database

Convert output of ibs.pairwise.db for plotting using DNAtools package

dists.product.pair

Distribution of product of several discrete random variables as product X*Y

IBD probabilities

Check if dist is properly specified for use with sim.q, exact.q

Allelic frequencies at 15 NGM loci

Computes distribution of KI for profiles with stated relationship

Retrieve the allele frequencies of a profiles object

ibs.pairwise.db.exp

Compute expected number of profiles pairs in a database that match fully and partially at each number of loci

Distribution of product of several discrete random variables

print profiles object

Retrieve the allele labels from the allele frequencies

ibs.pairwise.db

Pairwise comparison of all database profiles on IBS alleles

pr.next.alleles

Probability of seeing next alleles (Dirichlet sampling)

Sample random profile pairs with given relationship (sibs, parent/offspring, etc.)

Counts IBS alleles between profile pairs

profiles extract

profiles extract

ibs.pairwise.pr

Compute the probabilities that two profiles match a number of loci fully/partially

normalize.freqs

Normalizes allele frequencies such that their sum is 1

Computes Kinship Indices (KIs) for pairs of profiles

Recode allelic frequencies with different levels

ki.ibs.joint.dist

Computes joint distribution of KI and IBS for profiles with stated relationship

Probability of seeing next allele (Dirichlet sampling)

Computes KIs for case profile(s) with all database profiles

Computes CDF of KI between case profile and profile with stated relationship

sample.relatives

Sample random relatives of one profile or many profiles

Retrieve the markers of a profiles object

profiles.to.chars

Obtain STR repeat numbers of profiles as character matrix

Pre-computes KIs for use with ki.db function

Export to GenePop/LinkDos format

Allelic frequencies at 13 CODIS loci

profiles object

DNAprofiles-package

DNA profiles analysis

Computes distribution of number of IBS alleles for profiles with stated relationship

Estimate LR exceedance probabilities (with importance sampling)

Enumerate all attainable genotypes

CDF of product of a pair of distributions (one cumulative)

sample.profiles

Sample random unrelated profiles

For which markers is the profile homozygous/heterozygous?

Counts IBS alleles between case profile and all database profiles

Random match probability of profile(s)