4.1 Introduction to kin

kin computes kinship coefficients for pairs of pedigree members. It also computes single-locus and two-locus inbreeding coefficients for members of the pedigree. Briefly, the kinship coefficient between individuals i and j is the probability that a randomly-drawn allele from i is identical by descent (ibd) to randomly-drawn allele from individual j at the same locus. A single-locus inbreeding coefficient is the probability that an individual carries two copies of a gene that are ibd, at a given autosomal locus. In other words, an individual's single-locus inbreeding coefficient is equal to the kinship coefficient of his parents, as an individual's gametes can be thought of as random draws from his parents' chromosomes. A two-locus inbreeding coefficient is the probability that an individual carries two ibd copies of a gene at each of two linked loci. kin presents two-locus inbreeding coefficients as a function of the recombination fraction between the two loci.

Note: currently the kin program does not check for duplicate requests within a pedigree component of any inbreeding or kinship coefficients. It does check (and quits with an error) if a request is made for kinship of an individual with him/her self. These bugs will be fixed in a future MORGAN release.