4.4 kin statements

At least one of the following `compute ...' statements are required to run program kin. If there is more than one component (connected pedigree) in the file, the component number must be specified. MORGAN assigns component numbers to the connected pedigrees within the pedigree file. If your data set contains more than one component, you may first run pedcheck to determine which individuals are assigned which component numbers. pedcheck will sort by component number in the output pedigree file, although it will not list component numbers in the file. The screen output generated when running pedcheck will give component numbers and the number of individuals in each component. Check the error and warning messages when running kin to verify that component numbers were correctly specified. The program will quit if an individual's component number is incorrectly specified in the parameter file or if there is more than one component in the data set and no component is specified.

compute [component M] kinship coefficient N1 N2...

This statement names one or more pairs of pedigree members for which the kinship coefficient is to be computed.

compute [component M] inbreeding coefficient N1...

This statement names one or more pedigree members for whom the inbreeding coefficient is to be computed.

compute [component M] two-locus inbreeding coefficient N1...

This statement requests the computation of two-locus inbreeding coefficients, i.e. the probability of ibd at both loci, for the named individual. For the recombination frequencies at which the coefficients are computed, see the following statement.

set recombination frequencies X1 X2...

Two-locus inbreeding coefficients are computed for each of the list of recombination frequencies, in the range of 0.0 to 0.5. If frequencies are not given, the default values are: 0.0, 0.01, 0.04, 0.05, 0.10, 0.18, 0.30, and 0.50.