DNAprofiles: DNA Profiling Evidence Analysis
Version 0.3.1

Methods for studying forensic DNA profiling, in particular familial database searches.

AuthorMaarten Kruijver
Date of publication2015-04-21 10:02:51
MaintainerMaarten Kruijver <m.v.kruijver@vu.nl>
LicenseGPL (>= 2)
Version0.3.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DNAprofiles")

Getting started

Package overview

Popular man pages

dist.unique.events: Trim probability distribution to unique events with positive...
ibs.db: Counts IBS alleles between case profile and all database...
ibs.dist: Computes distribution of number of IBS alleles for profiles...
ibs.pairs: Counts IBS alleles between profile pairs
ibs.pairwise.pr: Compute the probabilities that two profiles match a number of...
ki.cdf: Computes CDF of KI between case profile and profile with...
ki.db: Computes KIs for case profile(s) with all database profiles
See all...

All man pages Function index File listing

Man pages

as.dbcompare: Convert output of ibs.pairwise.db for plotting using DNAtools...
check.dist: Check if dist is properly specified for use with sim.q,...
dist.pair.cdf: CDF of product of a pair of distributions (one cumulative)
dists.product: Distribution of product of several discrete random variables
dists.product.pair: Distribution of product of several discrete random variables...
dist.unique.events: Trim probability distribution to unique events with positive...
DNAprofiles-package: DNA profiles analysis
enum.profiles: Enumerate all attainable genotypes
est.freqs: Estimate allelic frequencies in reference database
exact.q: Compute exact LR exceedance probabilities
find.kth.element: Quickly finds the k'th largest element in a (large) vector
freqsNLngm: Allelic frequencies at 15 NGM loci
freqsNLsgmplus: Allelic frequencies at 10 SGMplus loci
freqsUScaucs: Allelic frequencies at 13 CODIS loci
get.freqs: Retrieve the allele frequencies of a profiles object
get.labels: Retrieve the allele labels from the allele frequencies
get.markers: Retrieve the markers of a profiles object
homozygous: For which markers is the profile homozygous/heterozygous?
ibdprobs: IBD probabilities
ibs.db: Counts IBS alleles between case profile and all database...
ibs.dist: Computes distribution of number of IBS alleles for profiles...
ibs.pairs: Counts IBS alleles between profile pairs
ibs.pairwise.db: Pairwise comparison of all database profiles on IBS alleles
ibs.pairwise.db.exp: Compute expected number of profiles pairs in a database that...
ibs.pairwise.pr: Compute the probabilities that two profiles match a number of...
ki: Computes Kinship Indices (KIs) for pairs of profiles
ki.cdf: Computes CDF of KI between case profile and profile with...
ki.db: Computes KIs for case profile(s) with all database profiles
ki.dist: Computes distribution of KI for profiles with stated...
ki.ibs.joint.dist: Computes joint distribution of KI and IBS for profiles with...
ki.precompute: Pre-computes KIs for use with 'ki.db' function
normalize.freqs: Normalizes allele frequencies such that their sum is 1
print.profiles: print profiles object
pr.next.allele: Probability of seeing next allele (Dirichlet sampling)
pr.next.alleles: Probability of seeing next alleles (Dirichlet sampling)
profiles: profiles object
profiles-extract: profiles extract
profiles.to.chars: Obtain STR repeat numbers of profiles as character matrix
recode.freqs: Recode allelic frequencies with different levels
rmp: Random match probability of profile(s)
sample.pairs: Sample random profile pairs with given relationship (sibs,...
sample.profiles: Sample random unrelated profiles
sample.relatives: Sample random relatives of one profile or many profiles
sim.q: Estimate LR exceedance probabilities (with importance...
write.genepop: Export to GenePop/LinkDos format

Functions

DNAprofiles Man page
DNAprofiles-package Man page
[.profiles Man page
as.dbcompare Man page
check.dist Man page
dist.pair.cdf Man page
dist.unique.events Man page
dists.product Man page
dists.product.pair Man page
enum.profiles Man page
est.freqs Man page
exact.q Man page
find.kth.element Man page
freqsNLngm Man page
freqsNLsgmplus Man page
freqsUScaucs Man page
get.freqs Man page
get.labels Man page
get.markers Man page
heterozygous Man page
homozygous Man page
ibdprobs Man page
ibs.db Man page
ibs.dist Man page
ibs.pairs Man page
ibs.pairwise.db Man page
ibs.pairwise.db.exp Man page
ibs.pairwise.pr Man page
ki Man page
ki.cdf Man page
ki.db Man page
ki.dist Man page
ki.ibs.joint.dist Man page
ki.precompute Man page
normalize.freqs Man page
pr.next.allele Man page
pr.next.alleles Man page
print.profiles Man page
profiles Man page
profiles extract Man page
profiles.to.chars Man page
recode.freqs Man page
rmp Man page
sample.pairs Man page
sample.profiles Man page
sample.relatives Man page
sim.q Man page
write.genepop Man page

Files

DNAprofiles
DNAprofiles/inst
DNAprofiles/inst/doc
DNAprofiles/inst/doc/exceedance-probabilities.R
DNAprofiles/inst/doc/exceedance-probabilities.Rmd
DNAprofiles/inst/doc/exceedance-probabilities.html
DNAprofiles/tests
DNAprofiles/tests/testthat.R
DNAprofiles/tests/testthat
DNAprofiles/tests/testthat/test_sample_relatives.R
DNAprofiles/tests/testthat/test_sample_profiles.R
DNAprofiles/tests/testthat/test_vectorchecks.R
DNAprofiles/tests/testthat/test_checkdist.R
DNAprofiles/tests/testthat/test_profiles_constructor.R
DNAprofiles/tests/testthat/ki_ibs_joint_dist_debug.R
DNAprofiles/tests/testthat/test_dirichlet_formula.R
DNAprofiles/tests/testthat/test_rmp_ki_consistent.R
DNAprofiles/tests/testthat/test_ki_distribution.R
DNAprofiles/tests/testthat/test_precomputed_ki.R
DNAprofiles/tests/testthat/test_ki.R
DNAprofiles/tests/testthat/test_homozygous.R
DNAprofiles/src
DNAprofiles/src/Makevars
DNAprofiles/src/dbcomparepairwise.cpp
DNAprofiles/src/Zprnextallele.cpp
DNAprofiles/src/findInt.cpp
DNAprofiles/src/kipairswithtable.cpp
DNAprofiles/src/kitargetsdbwithtable.cpp
DNAprofiles/src/dbcomparepairwisemc.cpp
DNAprofiles/src/sumprodxy.cpp
DNAprofiles/src/distproduct.cpp
DNAprofiles/src/rmp_old.cpp
DNAprofiles/src/countalleles.cpp
DNAprofiles/src/ki.cpp
DNAprofiles/src/allfinitepos.cpp
DNAprofiles/src/exactq.cpp
DNAprofiles/src/Zprnextalleles.cpp
DNAprofiles/src/rmp.cpp
DNAprofiles/src/rmpmat.cpp
DNAprofiles/src/Makevars.win
DNAprofiles/src/RcppExports.cpp
DNAprofiles/src/stl_nth_element.cpp
DNAprofiles/src/kiwithtable.cpp
DNAprofiles/src/distapprox.cpp
DNAprofiles/NAMESPACE
DNAprofiles/data
DNAprofiles/data/freqsNLsgmplus.rda
DNAprofiles/data/freqsNLngm.rda
DNAprofiles/data/freqsUScaucs.rda
DNAprofiles/R
DNAprofiles/R/ibs.pairwise.db.R
DNAprofiles/R/sample.R
DNAprofiles/R/check.dist.R
DNAprofiles/R/pr_next_allele.R
DNAprofiles/R/profiles.R
DNAprofiles/R/RcppExports.R
DNAprofiles/R/ki_precomp.R
DNAprofiles/R/kicdf.R
DNAprofiles/R/exactq.R
DNAprofiles/R/homozygous.R
DNAprofiles/R/ki.R
DNAprofiles/R/ki_ibs_dist.R
DNAprofiles/R/write.genepop.R
DNAprofiles/R/lrdist_cdf.R
DNAprofiles/R/profiles_extract.R
DNAprofiles/R/est.freqs.R
DNAprofiles/R/ibdprobs.R
DNAprofiles/R/rmp.R
DNAprofiles/R/misc.R
DNAprofiles/R/as.dbcompare.R
DNAprofiles/R/simq.R
DNAprofiles/R/freqs.R
DNAprofiles/R/ibs.R
DNAprofiles/R/lrdist.R
DNAprofiles/R/DNAprofiles-package.R
DNAprofiles/R/findk.R
DNAprofiles/vignettes
DNAprofiles/vignettes/exceedance-probabilities.Rmd
DNAprofiles/vignettes/vignettes.bib
DNAprofiles/README.md
DNAprofiles/MD5
DNAprofiles/build
DNAprofiles/build/vignette.rds
DNAprofiles/DESCRIPTION
DNAprofiles/ChangeLog
DNAprofiles/man
DNAprofiles/man/ibs.dist.Rd
DNAprofiles/man/print.profiles.Rd
DNAprofiles/man/ki.precompute.Rd
DNAprofiles/man/profiles-extract.Rd
DNAprofiles/man/pr.next.alleles.Rd
DNAprofiles/man/profiles.to.chars.Rd
DNAprofiles/man/recode.freqs.Rd
DNAprofiles/man/enum.profiles.Rd
DNAprofiles/man/ibs.pairwise.pr.Rd
DNAprofiles/man/homozygous.Rd
DNAprofiles/man/est.freqs.Rd
DNAprofiles/man/sample.relatives.Rd
DNAprofiles/man/dist.unique.events.Rd
DNAprofiles/man/DNAprofiles-package.Rd
DNAprofiles/man/ibs.db.Rd
DNAprofiles/man/ibs.pairs.Rd
DNAprofiles/man/exact.q.Rd
DNAprofiles/man/get.markers.Rd
DNAprofiles/man/ki.cdf.Rd
DNAprofiles/man/ki.dist.Rd
DNAprofiles/man/ibs.pairwise.db.exp.Rd
DNAprofiles/man/freqsNLsgmplus.Rd
DNAprofiles/man/pr.next.allele.Rd
DNAprofiles/man/rmp.Rd
DNAprofiles/man/as.dbcompare.Rd
DNAprofiles/man/check.dist.Rd
DNAprofiles/man/sample.profiles.Rd
DNAprofiles/man/ibdprobs.Rd
DNAprofiles/man/get.freqs.Rd
DNAprofiles/man/sample.pairs.Rd
DNAprofiles/man/ki.db.Rd
DNAprofiles/man/dist.pair.cdf.Rd
DNAprofiles/man/freqsUScaucs.Rd
DNAprofiles/man/normalize.freqs.Rd
DNAprofiles/man/freqsNLngm.Rd
DNAprofiles/man/ibs.pairwise.db.Rd
DNAprofiles/man/dists.product.Rd
DNAprofiles/man/find.kth.element.Rd
DNAprofiles/man/dists.product.pair.Rd
DNAprofiles/man/ki.Rd
DNAprofiles/man/get.labels.Rd
DNAprofiles/man/write.genepop.Rd
DNAprofiles/man/sim.q.Rd
DNAprofiles/man/profiles.Rd
DNAprofiles/man/ki.ibs.joint.dist.Rd
DNAprofiles documentation built on Jan. 15, 2017, 9:27 p.m.

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