buildPeds: Build all possible pedigrees In magnusdv/pedbuildr: Pedigree Reconstruction in R

Description

Build all possible pedigrees

Usage

 1 2 3 buildPeds(ids, sex, knownPO = NULL, allKnown = F, notPO = NULL, connected = F, maxLinearInbreeding = Inf, genderSym = F, verbose = F)

Arguments

 ids A vector of ID labels sex A vector of the same length as ids, with entries 1 (male) or 2 (female) knownPO A list of pairs of ID labels: The known parent-offspring pairs allKnown A logical. If TRUE, no other pairs than knownPO will be assigned as parent-offspring. If FALSE (default), all pairwise combinations of ids - except those in notPO - will be treated as potential parent-offspring pairs. notPO A list of pairs of ID labels: Pairs known not to be parent-offspring. connected A logical; if TRUE only connected pedigrees are returned. Default: FALSE. maxLinearInbreeding A nonnegative integer, or Inf (default). If this is a finite number, it disallows mating between pedigree members X and Y if X is a linear descendant of Y separated by more than the given number. For example, setting maxLinearInbreeding = 0 forbids mating between parent-child, grandparent-grandchild, a.s.o. If maxLinearInbreeding = 1 then parent-child matings are allowed, but not grandparent-grandchild or higher. genderSym A logical. If TRUE, pedigrees which are equal except for the gender distribution of the added parents, are regarded as equivalent, and only one of each equivalence class is returned. Example: paternal vs maternal half sibs. verbose A logical

A list

Examples

 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 p = buildPeds(1:3, sex = c(1,2,1), knownPO = list(c(1,3), c(2,3))) stopifnot(length(p) == 26) # plotPeds(p) # Remove duplicates coming from gender swaps among added parents. # Only one such duplicate here: where 1 and 2 are paternal/maternal half sibs p2 = buildPeds(1:3, sex = c(1,2,1), knownPO = list(c(1,3), c(2,3)), genderSym = TRUE) stopifnot(length(p2) == 25) # plotPeds(p2) # Remove pedigrees with linear inbreeding (e.g. parent-child) p3 = buildPeds(1:3, sex = c(1,2,1), knownPO = list(c(1,3), c(2,3)), maxLinearInbreeding = 0) stopifnot(length(p3) == 8) # plotPeds(p3)

magnusdv/pedbuildr documentation built on Oct. 9, 2019, 2:51 p.m.