rres (version 1.1)

ibd.proportion: Score IBD proportion.

Description

ibd.proportion returns the proportion of IBD sharing between two haplotypes of the same individual or two individuals.

Usage

ibd.proportion(inheritance, ind1index, ind2index = NULL, startpos = NULL,
  endpos = NULL)

Arguments

inheritance

list of matrices.

ind1index, ind2index

positive integer.

startpos, endpos

non-negative number.

Value

A value between 0 and 1 representing the proportion of IBD segment.

Details

When only one individual index is supplied, ibd.proportion returns the realized inbreeding coefficient of the individual. When two individual indices are supplied, ibd.proportion returns the realized relatedness of the two individuals.

Examples

# NOT RUN {
# 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)

# realized inbreeding of inbred child
get.pedindex(pedinfo, "31")
ibd.proportion(inheritance, 5)

# realized relatedness between individual 21 and 22 (parents of inbred child)
get.pedindex(pedinfo, c("21", "22"))
ibd.proportion(inheritance, 3, 4)
# }