ibd.length: Score IBD length.

In bowenwang7/rres: Realized Relatedness Estimation and Simulation

Description

ibd.length returns the total length of IBD segemnt between two haplotypes.

Usage

ibd.length(inher.hap1, inher.hap2, startpos = NULL, endpos = NULL)

Arguments

inher.hap1, inher.hap2	numeric matrix.
startpos, endpos	non-negative number.

Details

This function works with output from sim.recomb.

Value

A non-negative number representing the length of IBD segment in Haldane centiMorgan.

Examples

# a simple pedigree with sibling marriage
pedigree = as.character(rep(1, 5))
member = as.character(c(11, 12, 21, 22, 31))
sex = as.numeric(c(1, 2, 1, 2, 1))
father = as.character(c(NA, NA, 11, 11, 21))
mother = as.character(c(NA, NA, 12, 12, 22))
pedinfo = data.frame(pedigree, member, sex, father, mother, stringsAsFactors = FALSE)
inheritance = sim.recomb(pedinfo, 100)

# IBD length between the two haplotypes of inbred individual 31
ibd.length(inheritance[[9]], inheritance[[10]])

bowenwang7/rres documentation built on May 5, 2019, 2:41 a.m.