reconstruct: Pedigree reconstruction In magnusdv/pedbuildr: Pedigree Reconstruction in R

Description

Reconstruct the most likely pedigree from genotype data

Usage

 1 2 reconstruct(alleleMatrix, loci, pedlist = NULL, pairwise = F, founderInb = 0, sortResults = T, verbose = T, ...)

Arguments

 alleleMatrix A matrix with two columns for each marker loci A list of marker attributes pedlist A list of pedigrees. If NULL, buildPeds() is used to generate a list pairwise A logical. If TRUE, an initial stage of pairwise IBD estimation is done, in order to infer certain parent-child pairs, as well as certain non-parent-child pairs. When this option is used, arguments to knownPO and notPO are ignored founderInb A number in the interval [0,1], used as background inbreeding level in all founders sortResults A logical. If TRUE, the output is sorted so that the most likely pedigree comes first verbose A logical; verbose output or not ... Additional parameters passed on to buildPeds()

Value

A list with two entries:

• pedlist : A list of pedigrees. This equals (except possibly for sorting) the input argument pedlist if this was given. If sortResults = TRUE then the list is sorted so that the most likely pedigrees come first

• logliks : A numerical vector containing the pedigree log-likelihoods

• alleleMatrix The input allele matrix

Examples

 1 2 3 4 5 6 7 8 9 10 11 12 13 # Simulate genotype data for a trio family (increase N!) x = forrel::markerSim(nuclearPed(1), N = 50, alleles = 1:3, seed = 123) # Extract allele matrix and locus attributes (frequencies a.s.o.) m = getAlleles(x) loci = lapply(x\$MARKERS, attributes) # Reconstruct the most likely pedigree from the data res = reconstruct(m, loci, sex = c(1, 2, 1), connected = TRUE, genderSym = TRUE, pair=TRUE) # Plot the best pedigrees plotBestPeds(res)

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