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Assign Family IDs

FindFamilies.Rd

Find clusters of connected individuals in a pedigree, and assign each cluster a unique family ID (FID).

Usage

FindFamilies(Pedigree = NULL, SeqList = NULL, MaybeRel = NULL)

Arguments

Pedigree

dataframe with columns id - parent1 - parent2; only the first 3 columns will be used.

SeqList

list as returned by sequoia. If Pedigree is not provided, the element Pedigree from this list will be used if present, and element Pedigreepar otherwise.

MaybeRel

Output from GetMaybeRel, a dataframe with probable but non-assigned relatives.

Value

A numeric vector with length equal to the number of unique individuals in the pedigree (i.e. number of rows in pedigree after running

PedPolish on Pedigree).

Details

This function repeatedly finds all ancestors and all descendants of each individual in turn, and ensures they all have the same Family ID. Not all connected individuals are related, e.g. all grandparents of an individual will have the same FID, but will typically be unrelated.

When UseMaybeRel = TRUE, probable relatives are added to existing family clusters, or existing family clusters may be linked together. Currently no additional family clusters are created.

See also

GetAncestors, GetDescendants, getGenerations

Examples


PedG <- SeqOUT_griffin$PedigreePar[,1:3]
FID_G <- FindFamilies(PedG)
PedG[FID_G==4,]
#>             id         dam        sire
#> 6  i014_2001_F        <NA>        <NA>
#> 10 i018_2001_M        <NA>        <NA>
#> 15 i025_2002_M i014_2001_F i018_2001_M
#> 37 i057_2003_M        <NA> i018_2001_M
#> 53 i078_2004_M        <NA> i025_2002_M
#> 64 i094_2005_M        <NA> i078_2004_M
#> 93 i135_2007_F        <NA> i078_2004_M