High-Performance Open-Source Archive
The dataset FORCE, containing positions and allele frequencies for the FORCE SNP panel (Tillmar et al, 2021, doi:10.3390/genes12121968)), has been updated to include 15 SNPs that were previously excluded due to missing frequency information. The current dataset contains all of the 3931 autosomal kinship SNPs in the original publication, except 1 (rs2323964) which is no longer supported by dbSNP.
A new dataset XFORCE has been added, annotating the 246 X-chromosomal SNPs on the FORCE panel.
The function checkPairwise() gains a new argument
legendData making it easier to customise the
legend.
New function rankProfiles() predicting the most
likely profile of an untyped pedigree member.
In oneMarkerDistribution and
twoMarkerDistribution, the argument
partialmarker has been renamed to
marker.
In profileSim() and markerSim(), the
argument ids can be the name of a function, e.g.,
leaves.
kinshipLR gains argument likArgs for
passing arguments to pedprobr::likelihood(). The motivation
for this is to give access to the special lumping methods recently
implemented in pedprobr, for example
kinshipLR(..., likArgs = list(special = TRUE, alleleLimit = 20)).
New argument acrossComps in
ibdEstimate() and checkParwise().
readFam() is no longer exported from forrel; see
pedFamilias::readFam().
Minor improvements and bug fixes in
checkPairwise().
Minor updates of README and docs.
The function checkPairwise() has undergone
substantial revision, with plots implemented in both
ggplot2 and plotly in addition to the
default base plot. A summary of the main changes are:
plotType can be either “base” (default),
“ggplot” or “plotly”plotCP() which is also exportedids, which when given restricts the
checks to those individualsLR is renamed to GLR
(generalised likelihood ratio)pedrel describing (in words) each
relationship according to the pedigree. The descriptions are obtained
with the verbalisr packagensim, pvalThreshold and seed. By
default nsim = 0, meaning that no simulations are
performed. The P-values are stored in the output column
pval.New function quickLR() performs the most common
kinship tests (paternity and sibship) for a pair of
individuals.
New function ibdLoglik() computes the pairwise
likelihood for given set IBD coefficients (kappa or delta).
Improved progress bars using the pbapply
package.
Removed (long deprecated) IBDtriangle(), replaced by
ribd::ibdTriangle().
Improved missingPersonPlot() appearance.
In ibdEstimate(), more efficient data prep, and
better removal of missing data.
Refresh code in examples.
Functions facilitating interaction with the Familias software
have been moved to a dedicated package, pedFamilias.
However, readFam() and writeFam() will
continue to be re-exported from forrel for some
time.
Remove dependency of pedmut.
In kinshipLR(), improve checking of argument
markers.
New function writeFam().
readFam() gains argument fallbackModel
to be applied if the function encounters unrecognisable mutation models
in the .fam file.
Remove use of packageVersion() (thereby sidestepping
CRAN issue).
Use pedtools::setMutmod() instead of
pedprobr::setMutationModel().
Update version requirements for imported packages.
readFam() includes more input checks and gives better
error/warning messages.readFam() now handle all mutation models available
in the Familias software.
readFam() and Familias2ped() gain
argument prefixAdded.
missingPersonLR() manifesting when POI and
MP have identical names.Added license statement GPL (>=2).
Expanded README, adding an example with conditional simulation.
Updated package documentation.
Fixed CRAN note by avoiding ibdsim2:::.
profileSim(x, N = 1) is now a
single pedigree, instead of a list of length 1 (containing the
pedigree). This is usually the desired output of N = 1 in
interactive use. To override this behaviour, set
simplify1 = FALSE.Added dataset FORCE describing the FORCE snp panel (Tillmar et al, 2021, doi:10.3390/genes12121968).
profileSim() has a new argument
simplify1 (by default TRUE) controlling the output when
N = 1.
profileSim() now allows markers to be a
list of frequency vectors, simplifying the code in unconditional
simulations. For instance, the following command now works:
nuclearPed() |> profileSim(markers = NorwegianFrequencies).
Previously this required an intermediate step of
setMarkers().
In kinshipLR() the treatment of linked markers (with
MERLIN) has been rewritten and is substantially more efficient. A new
argument keepMerlin allows to keep merlin files for
debugging.
missingPersonLR() was overhauled, making it more
user friendly.
missingPersonPlot() has been modified and updated in
sync with changes in pedtools.
inherits() instead of
class().New function findExclusions() for identifying
incompatible markers in identification cases.
powerPlot() gains a logical argument
jitter, which can be switched on to avoid
overplotting.
checkPairwise() gains an argument
excludeInbred, which is TRUE by default. This is sensible
since the plot shows estimated kappa coefficients, which are
well-behaved only for pairs of noninbred individuals.
forrel now requires R version 4.1 and recent versions of pedtools and ribd. This allowed many simplifications in code and examples.
Added scales as a suggested package.
The new function ibdEstimate() replaces the previous
IBDestimate() (note the name change). This is a complete
rewrite, which optimises the log-likelihood using a projected gradient
descent algorithm, combined with a version of Armijo line
search.
The function ibdBootstrap() replaces the previous
kappaBootstrap() and deltaBootstrap(), and is
considerably faster. This function implements both parametric and
non-parametric bootstrap, controlled with the method
parameter.
The output of ibdEstimate() now has a class
attribute “ibdEst”, with its own print and subsetting methods.
kinshipLR() now handles linked markers by wrapping
MERLIN.
New functions kappaBootstrap() and
deltaBootstrap() for assessing the uncertainty of pairwise
relatedness estimates.
New function randomPersonEP() handling a common
special case of exclusionPower().
forrel now depends on version 0.9.6 (or later) of pedtools.
Deprecated arguments id.labels and
frametitles in missingPersonPlot() has been
removed.
Implement parallelisation in profileSim().
Partial rewrite of kinshipLR(), including new
argument source.
Added the NorwegianFrequencies dataset, containing
allele frequencies for 35 STR markers.
New function missingPersonLR().
New function checkPairwise() replaces the (long
obsolete) examineKinships().
New functions markerSimParametric() and
profileSimParametric() for simulating marker data for two
individuals with given kappa (or condensed identity)
coefficients.
profileSim(), fix bug resulting in identical seeds
given to each parallel cluster.readFam() now has a parameter Xchrom
which can be used to indicate that the markers included in the file are
on the X chromosome
MPPsims() is more flexible, and allows subsetting of
its output.
powerPlot() is more flexible and allows finer
control of the plot contents
readFam(). It is more robust
now, and fails gracefully in certain situations which cannot currently
be handled (e.g. if the file contains twins).
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