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pedprobr 0.9.5

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@magnusdv magnusdv released this 19 Mar 14:05
v0.9.5
7bf091b

  • oneMarkerDistribution() now fully supports pedigrees with multiple components.

  • oneMarkerDistribution() has a new argument output taking values "array" (default, as before), "table", or "sparse". Both "table" and "sparse" produce data frames where each row corresponds to a genotype combination. The "sparse" format only includes combinations with non-zero probability.

  • In oneMarkerDistribution(), the argument partialmarker has been renamed to marker. The old name still works as an alias, but will be removed in a future version. While the old argument had no default value, the new defaults to the first attached marker. This simplifies the call in many cases, for example singleton("A") |> addMarker() |> oneMarkerDistribution("A").

  • In twoMarkerDistribution(), the arguments partialmarker1 and partialmarker2 have been renamed to marker1 and marker2, respectively.

  • Fixed bug affecting likelihood calculations in pedigrees with partial genotypes (e.g. "1/-") in founders.

  • The function allGenotypes() is ~2-4 times faster due to a better implementation.

  • Updated dependencies: pedtools v2.6.0, pedmut v0.7.0.

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