Sib-pair Command: set locus


ClassData Declaration command
Nameset 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
affectionbinary trait
categoricalcategorical 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)


<< (set checking)Up to index>> (declare loci)