DNAprofiles: DNA Profiling Evidence Analysis

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

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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

Files in this package

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

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