ibd.proportion: Score IBD proportion.
In bowenwang7/r3: Realized Relatedness Estimation and Simulation

Description Usage Arguments Details Value Examples

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

1 2	ibd.proportion(inheritance, ind1index, ind2index = NULL, startpos = NULL, endpos = NULL)

`inheritance`	list of matrices.
`ind1index, ind2index`	positive integer.
`startpos, endpos`	non-negative number.

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.

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

# 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)