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pedtools 2.10.0

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@magnusdv magnusdv released this 01 Feb 16:36
v2.10.0
c629e0a

  • New function addSibling() for adding a sibling to an existing pedigree member.

  • New function isHomozygous() for finding and counting homozygous genotypes in the marker data.

  • New function sameGenotype() for finding and counting markers for which two individuals have the same genotype.

  • New functions expectedHomozygosity() and expectedHeterozygosity() for computing these quantities from allele frequencies (or marker objects).

  • Extracting sub-pedigrees with subset() is now more flexible, allowing disconnected outputs. It also has a new argument missingParents controlling how to handle parents that are not included in the subset.

  • The branch() behaves more intuitively thanks to the improved subset.ped().

  • alleles(x, marker) now accepts multiple markers at once, returning a list of character vectors.

Other

  • father(x, id) and mother(x, id) now output NA when id is a founder in x. (Previously this gave character(0).)
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