Skip to content

pedtools 2.7.0

Compare
Choose a tag to compare
@magnusdv magnusdv released this 28 Jun 12:26

New features

  • plot.ped() gains a new argument, spouseOrder, to specify the display order of spouses.

  • readPed() and as.ped() now include a addMissingFounders argument, supporting pedigree files where (some or all) founders are not explicitly listed (i.e., entries in the fid or mid columns that do not appear in the id column).

  • readPed() and as.ped() now also feature a sexCodes argument, accommodating pedigree files where sex is indicated by codes other than the standard 0 (unknown), 1 (male), 2 (female).

  • reorderPed() has improved flexibility, allowing the reordering of a subset of the pedigree.

  • selfingPed() now accepts a vector of ID labels as the first argument. (Previously, only the number of selfings could be given.)

  • The plotting argument showEmpty, controlling the appearance of missing genotypes, now accepts a function, e.g. leaves().

Other changes

  • getComponent() behaves better when the pedigree has only one component.

  • ped() checks for illegal sex entries earlier than before, thus avoiding certain (rare) problems.

  • Brush up on code and documentation.