findDFC: Finds the double first cousins in a pedigree

In matthewwolak/nadiv: (Non)Additive Genetic Relatedness Matrices

Finds the double first cousins in a pedigree

Description

Given a pedigree, all pairs of individuals that are double first cousins are returned.

Usage

findDFC(
  pedigree,
  exact = FALSE,
  parallel = FALSE,
  ncores = getOption("mc.cores", 2L)
)

Arguments

pedigree	A pedigree with columns organized: ID, Dam, Sire
exact	A logical statement indicating if individuals who are exactly double first cousins are to be identified
parallel	A logical statement indicating if parallelization should be attempted. Note, only reliable for Mac and Linux operating systems.
ncores	Number of cpus to use, default is maximum available

Details

When exact = TRUE, only those individuals whose grandparents are completely unrelated will be identified as double first cousins. When exact = FALSE, as long as the parents of individuals i and j are two sets of siblings (i.e., either sires full brothers/dams full sisters or two pairs of opposite sex full sibs) then i and j will be considered double first cousins. In the event where the grandparents of i and j are also related, exact = FALSE will still consider i and j full sibs, even though genetically they will be more related than exact = TRUE double first cousins.

parallel = TRUE should only be used on Linux or Mac OSes (i.e., not Windows).

Value

a list:

PedPositionList

gives the list of row numbers for all the pairs of individuals that are related as double first cousins.

DFC

gives the list of IDs, as characters, for all the pairs of individuals that are related as double first cousins.

FamilyCnt

If two individuals, i and j, are double first cousins, then i's siblings will also be double first cousins with j's siblings. Therefore, this is the total number of family pairs where offspring are related as double first cousins.

Author(s)

[e-mail]

matthewwolak/nadiv documentation built on July 7, 2023, 1:24 p.m.