DNAprofiles: DNA Profiling Evidence Analysis

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

Author
Maarten Kruijver
Date of publication
2015-04-21 10:02:51
Maintainer
Maarten Kruijver <m.v.kruijver@vu.nl>
License
GPL (>= 2)
Version
0.3.1

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

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