getGenerations: Count Generations

In sequoia: Pedigree Inference from SNPs

Count Generations

Description

For each individual in a pedigree, count the number of generations since its most distant pedigree founder.

Usage

getGenerations(Ped, StopIfInvalid = TRUE)

Arguments

Ped	dataframe, pedigree with the first three columns being id - dam - sire. Column names are ignored, as are additional columns.
StopIfInvalid	if a pedigree loop is detected, stop with an error (TRUE, default) or return the Pedigree, to see where the problem(s) occur.

Value

A vector with the generation number for each individual, starting at 0 for founders. Offspring of G0 X G0 are G1, offfspring of G0 X G1 or G1 x G1 are G2, etc. NA indicates a pedigree loop where an individual is its own ancestor (or that the pedigree has >1000 generations).

If no output name is specified, no results are returned, only an error message when the pedigree contains a loop.

See Also

GetAncestors, GetDescendants to get all ancestors resp. descendants of a specific individual (with a warning if it is its own ancestor); FindFamilies to find connected sub-pedigrees.

Examples

# returns nothing if OK, else error:
getGenerations(SeqOUT_griffin$Pedigree)

# returns vector with generation numbers:
G <- getGenerations(SeqOUT_griffin$Pedigree, StopIfInvalid=FALSE)
table(G, useNA='ifany')
Ped_plus_G <- cbind(SeqOUT_griffin$Pedigree, G)

sequoia documentation built on Sept. 8, 2023, 5:29 p.m.