ibd.proportion {rres} | R Documentation |
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. |
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.
Value
A value between 0 and 1 representing the proportion of IBD segment.
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)
# 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)
[Package rres version 1.1 Index]