forrel - forrel 1.8.1

New features

• 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.

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Published by magnusdv 12 months ago

forrel - forrel 1.8.0

New features

• 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)).

Other

• Updated dependencies to pedtools 2.8.1, pedmut 0.9.0 and pedprobr 1.0.0 (all related to special lumping).

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Published by magnusdv about 1 year ago

forrel - forrel 1.7.1

• 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.

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Published by magnusdv over 1 year ago

forrel - forrel 1.7.0

New features

• 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:

  • a new argument plotType can be either "base" (default), "ggplot" or "plotly"
  • the plotting is now done in a separate function plotCP() which is also exported
  • a new argument ids, which when given restricts the checks to those individuals
  • the output column LR is renamed to GLR (generalised likelihood ratio)
  • new output column pedrel describing (in words) each relationship according to the pedigree. The descriptions are obtained with the verbalisr package
  • estimation of P-values for each pairwise relationship, by parametric bootstrap simulations. This feature is controlled through new arguments nsim, 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.

Other

• 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.

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Published by magnusdv almost 2 years ago

forrel - forrel 1.6.1

• 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.

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Published by magnusdv over 2 years ago

forrel - forrel 1.6.0

New features

• New function writeFam().

• readFam() gains argument fallbackModel to be applied if the function encounters unrecognisable mutation models in the .fam file.

Other

• Remove use of packageVersion() (thereby sidestepping CRAN issue).

• Use pedtools::setMutmod() instead of pedprobr::setMutationModel().

• Update version requirements for imported packages.

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Published by magnusdv almost 3 years ago

forrel - forrel 1.5.2

New features

• readFam() includes more input checks and gives better error/warning messages.

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Published by magnusdv about 3 years ago

forrel - forrel 1.5.1

New features

• readFam() now handle all mutation models available in the Familias software.

• readFam() and Familias2ped() gain argument prefixAdded.

Bug fixes

• Fixed bug in missingPersonLR() manifesting when POI and MP have identical names.

Other

• Added license statement GPL (>=2).

• Expanded README, adding an example with conditional simulation.

• Updated package documentation.

• Fixed CRAN note by avoiding ibdsim2:::.

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Published by magnusdv about 3 years ago

forrel - forrel 1.5.0

Breaking changes

• The output of profileSim(x, N = 1) is now a single pedigree, instead of a list of length 1 (containing the pedigree). The new default is usually the desired object when N = 1 in interactive use. To override it, set simplify1 = FALSE.

New features

• Added dataset FORCE describing the FORCE snp panel (Tillmar et al, 2021, doi:10.3390/genes12121968).

• 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().

• profileSim() has a new argument simplify1 (by default TRUE) controlling the output when N = 1.

• 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.

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Published by magnusdv over 3 years ago

forrel - forrel 1.4.1

New features

• 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.

Other changes

• 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.

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Published by magnusdv over 4 years ago

forrel - forrel 1.3.0

New features

• 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.

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Published by magnusdv over 5 years ago

forrel - forrel 1.2.0

New features

• 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().

Other changes

• forrel now depends on version 0.9.6 (or later) of pedtools

• Removed deprecated arguments id.labels and frametitles in missingPersonPlot().

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Published by magnusdv over 5 years ago

forrel - forrel 1.1.0

New features

• 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.

Bug fixes

• In profileSim(), fix bug resulting in identical seeds given to each parallel cluster.

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Published by magnusdv over 5 years ago

forrel - forrel 1.0.1

New features

• 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

Bug fixes

• Fixed several glitches in 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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Published by magnusdv over 6 years ago

forrel - forrel 1.0.0

Initial CRAN release

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Published by magnusdv over 6 years ago