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

View on CRAN

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

as.dbcompare Man page
check.dist Man page
dist.pair.cdf Man page
dists.product Man page
dists.product.pair Man page
dist.unique.events Man page
DNAprofiles Man page
DNAprofiles-package 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
print.profiles Man page
pr.next.allele Man page
pr.next.alleles Man page
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

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Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.