For example, if you wanted to calculate the relatedness of queens to workers, the Px Set would be the queens. The Py Set for each queen would be the workers on her nest. This would be a different set for each queen (except for any that were on the same nest). However the user would not need to define the Py Set separately for each queen; the Py Set would just be "workers."
In scoring autorads, alleles are generally identified by their length. A locus thus might have alleles 109, 112 and 118 (for example) and an individual's genotype would be written 109/112. To enter this data into a relatedness data set, you name the alleles with lowercase letters. So 109 becomes a, 112 becomes b, and 118 becomes c. The genotype of the example individual above is then written ab.
The letter x is reserved to indicate missing information, so if you lack a genotype for an individual at some locus, you would enter xx for that individual at that locus. In converting allele names to characters, you should go alphabetically. If the program finds, for example, an allele f in the population, it will allocate memory for allele frequencies for alleles a - e even if f is the first allele present.
The easiest way to create a text data file for the program is with a spreadsheet application such as Excel. You can also create readable files with any word processor, if you are careful to keep track of the number of tabs (used to separate columns). A data file can contain comment lines, indicated by a leading asterisk, in addition to the actual data. The first non-comment line in the file must contain the variable names for each column, and subsequent lines carry the information for each individual. Variables can be in any order or in any column; the only restriction is that all loci be in one set of consecutive columns.
To load a text file, you start by choosing Configure from the File menu in the Relatedness application. This gives you a dialog which has check boxes to identify what variables your data file includes, and what column each variable is in. The program remembers the last-used settings in this box, so if you have data files in a standard format you will not need to specify the settings every time. Once you have set the configuration, choose Open text in the File menu to read the file.
There are sets of operators for each subgroup variable, and boolean AND and OR operators to combine the different subgroup tests into a single true/false value.The user chooses an operator from the row of radio buttons, and enters a value or list of values in the box just beneath the row to define what values will be compared to. The result is a boolean true/false value which indicates whether the individual being tested meets the definition or not. The checkboxes on the left indicate whether the subgroup variable is active or not; if unchecked, then that variable will not be used in any tests.
For example, if you want the Px set to be "all individuals older than 3 days", you would (for the subgroup variable "age") pick the operator ">" and enter 3 into the text box.
The dialog box for the Py Set is similar to the Px dialog, but has some extra operators allowing the user to specify tests such as "values equal to the value of the current X individual."
The Relatedness 4.2 Manual describes all of the operators in detail. Refer to it for further information.
This dialog allows you to select options for the calculation. On the left are the available statistics, which include relatedness, some F-statistics for measuring inbreeding, and a statistical test of difference between two different relatedness values. On the right are options concerning the calculation: the program can calculate an average value for the whole population, or values separate for each group and/or each locus. The program can also calculate "Jackknife" statistics. These are standard error estimates for the selected statistics. See the manual for more information about these options.
Once you've picked your options, click Okay and the program will go to work on the calculations. When it's done it will put up a window with a full report on its results. These results can either be saved to disk or printed, as well as read from within the program.