pedprobr - pedprobr 0.9.4

• Fixed rare bug in the peeling algorithm manifesting with reversed peeling order.

• pedtools v2.2.0 is now required.

- R
Published by magnusdv about 2 years ago

pedprobr - pedprobr 0.9.3

• Fix bug in likelihood() affecting singleton with partial genotype (e.g. "1/-").

• Minor optimisations in reduceAlleles() and startdata_M().

• More efficient oneMarkerDistribution() and twoMarkerDistribution() in cases without mutation models.

• README updates.

- R
Published by magnusdv over 2 years ago

pedprobr - pedprobr 0.9.2

The version implements several improvements in the peeling algorithm, mostly invisible to end users (except that likelihoods calculations will be noticeably faster, and use much less memory, in many cases).

• Less memory footprint for untyped founders with only 1 child: Sample alleles directly, avoid complete set of genotypes.

• Avoid costly 3-dimensional arrays in peeling calculations.

• More efficient genotype elimination in likelihood calculations involving markers without mutation modelling. As a result, this is now enforced (rather than optional) everywhere, and the eliminate argument is deprecated.

• Added citation info.

- R
Published by magnusdv over 2 years ago

pedprobr - pedprobr 0.8.0

New features

• Mutation models are now supported in likelihood2(), which calculates pedigree likelihoods given data from two linked markers.

• New functions haldane() and kosambi().

Other

• Update README.

• Update package doc.

• Include license (GPL >= 2).

- R
Published by magnusdv over 3 years ago

pedprobr - pedprobr 0.7.1

• reduceAlleles() is faster in some cases, due to the new pedmut::lumpedModel()

• A few minor speedups and code improvements

- R
Published by magnusdv over 3 years ago

pedprobr - pedprobr 0.7.0

This release introduces a number of minor improvements of the interaction with the external software MERLIN used for analysis of linked markers (https://csg.sph.umich.edu/abecasis/merlin/index.html).

New features

• merlin() gains argument checkpath, which can be set this to FALSE to avoid redundant checks of MERLIN availability.

• likelihoodMerlin() gains argument perChrom, used to parse the chromosome-wise likelihoods from the MERLIN output.

• lumpAlleles() gains argument always. By default lumping is skipped for markers where all individuals are genotyped, but this can cause problems e.g. with MERLIN which operates with an upper limit of allleles.

• Some efforts are done to check for (and warn about) underflow/overflow in MERLIN results.

- R
Published by magnusdv about 4 years ago

pedprobr - pedprobr 0.6.1

Bug fixes

• Fixed a regression error involving the external program MINX (part of MERLIN). The new version of checkMerlin() by default checks that both merlin and minx are available on the system, and that they come from the latest MERLIN version.

- R
Published by magnusdv over 4 years ago

pedprobr - pedprobr 0.6.0

Breaking changes

• pedprobr now depends on R 4.1 and pedtools 1.1.0.

• The deprecated argument loop_breakers has been completely removed (renamed to loopBreakers)

New features

• likelihood.ped() gains a new argument lump, which activates allele lumping. This is TRUE by default, and should remain so in most cases.

• Using theta correction in pedigrees with inbred founders now gives an error.

• The internal peelingProcess() now checks for unbroken loops in the pedigree. (Of interest for developers mainly.)

Bug fixes

• Fixed bug affecting likelihood computations with theta correction.

Other changes

• When calling MERLIN, the window-centric and unnecessary .exe extensions has been removed.

• Many examples have been rewritten in simpler code, taking advantage of pedtools::addMarker and the pipe |>.

- R
Published by magnusdv over 4 years ago

pedprobr - pedprobr 0.5.0

New features

• Simplify removal of mutation models, with setMutationModel(..., model = NULL).

Bug fixes

• Fixed bug in setMutationModel() affecting lists of multiple pedigrees.

- R
Published by magnusdv over 5 years ago

pedprobr - pedprobr 0.4.0

Breaking changes

• likelihood() has been refactored, and the functionality for calculating the likelihood of two linked markers is moved to a separate function, likelihood2().

New features

• Theta correction is implemented in likelihood calculations, through the argument theta of likelihood().

• merlin() and likelihoodMerlin() have been overhauled.

• A new function checkMerlin() checks if MERLIN is installed and available.

• merlin() now has an argument linkageMap for describing linked markers.

• likelihoodMerlin() gains arguments logbase (for log output) and rho (as a simpler alternative to linkageMap).

• New function lumpAlleles().

- R
Published by magnusdv over 5 years ago

pedprobr - pedprobr 0.2.0

New features

• New general MERLIN wrapper, merlin().

• Both likelihoodMerlin() and the new merlin() now accepts ped lists.

Bug fixes

• Fixed a bug affecting lumped mutation models.

- R
Published by magnusdv over 6 years ago

pedprobr - pedprobr 0.1.0

Initial CRAN release

- R
Published by magnusdv over 6 years ago