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magnusdv / pedtools

Tools for working with pedigrees in R
GNU General Public License v3.0
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Unplottable pedigrees #3

Closed magnusdv closed 1 year ago

magnusdv commented 6 years ago

The class of pedigrees allowed in pedtools is larger than for the kinship2 package, which does the plotting. Hence certain pedigrees cannot be plotted as of yet. In particular this concerns pedigrees with selfing:

x = pedtools::ped(1:2, fid=c(0,1), mid=c(0,1), sex=c(0,1))
x
#>  id fid mid sex
#>   1   *   *   0
#>   2   1   1   1
plot(x)
#> Warning in kinship2::pedigree(id = ped$id, dadid = ped$fid, momid =
#> ped$mid, : More than 25% of the gender values are 'unknown'
#> Error in kinship2::pedigree(id = ped$id, dadid = ped$fid, momid = ped$mid, : pedigree must have at least 2 founders

And a different error here:

library(pedtools)
y = nuclearPed(1, sex = 0)
y = addChildren(y, father = 3, mother = 3, nch = 1)
y
#>  id fid mid sex
#>   1   *   *   1
#>   2   *   *   2
#>   3   1   2   0
#>   4   3   3   1
plot(y)
#> Error in kinship2::pedigree(id = ped$id, dadid = ped$fid, momid = ped$mid, : Id not male, but is a father: 3
magnusdv commented 5 years ago

Idea: Plot the marriage graph in these cases?

magnusdv commented 1 year ago

Closing this as resolved; these pedigrees are now automatically plotted as DAGs.