reconstruct: Pedigree reconstruction

Description Usage Arguments Value Examples

View source: R/reconstruct.R

Description

Reconstruct the most likely pedigree from genotype data

Usage

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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:

Examples

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# 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.