| Class | Data Declaration command |
| Name | set locus |
| Arguments | <locus name> <locus type> [<map position> [<description...>]] |
Declares position (by order within list), name and type of locus within
pedigree file. Locus type may be either:
| marker | an autosomal (fully) codominant marker |
| xmarker | X-linked codominant marker |
| haploid | Y or mitochondrial codominant marker |
| quantitative | quantitative (or interval or ordinal) trait |
| affection | binary trait |
| categorical | categorical trait |
It is best to avoid a locus name containing reserved characters (eg "+-*/()^"), if algebraic manipulation of that variable will be required (otherwise quotation of the name is required). Names identical to commands also cause trouble unless protected by brackets.
The fifth column (optionally) contains the genetic map position. All subsequent words (up to a total of 40 characters) are stored as an annotation. The annotation is appended to the long form of output of some commands (eg show loci or list), and is searchable by some commands (currently keep|drop where). If you wish to annotate, but do not have a map position, a "." for the fifth column is unobtrusive and accepted by Sib-pair.
The annotation for a categorical variable can also include labels for the levels of the trait. These are of the form "level=label".
Example:
>> set loc ibd aff . Inflammatory bowel disease >> set loc D16S769 mar 53.713 26066263 bp (chr 16) >> list Locus Type Position --------------- ---- ---------- ibd a 6 Inflammatory bowel disease D16S769 m 7-- 8 26066263 (chr 16)
>> set loc eyecol cat . 1=blue 2=green 3=brown
[...]
>> tab eyecol
------------------------------------
Tabulation of "eyecol "
------------------------------------
eyecol Count Percent
-----------------------------
blue 5782 42.9
green 4538 33.6
brown 3171 23.5
-----------------------------
Total 13491 (and 13592 missing)
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