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help for ^gencc^, ^gencci^                                             (statalist )
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Case-control studies for genetic epidemiologists
-------------------------------------------------

 ^gencc^ locus1 locus2 [weight] [^if^ exp] [^in^ range], group(casevar) 
		         	      	        [ ^l^evel^(^#^)^ ^e^xact ^tb^ ^w^oolf ]

 ^gencci^ #a #b #c #d [^,^ ^l^evel^(^#^)^ ^e^xact ^tb^ ^w^oolf ]


Description
-----------

^gencc^ is used with case-control genetic studies.  Point estimates and
confidence intervals for the odds ratio are calculated along with attributable
or prevented fractions for those with the allele being examined and total
population.  ^gencci^ is the immediate form of ^gencc^; see help @immed@.  Also
see help  @symmetry@ for related commands.

^gencc^ will produce one output table for each allele in the data.

Options
-------

^level(^#^)^ specifies the confidence level, in percent, for confidence intervals;
    see help @level@.

^exact^ requests Fisher's exact p be calculated rather than the chi-squared and
    its significance level.  We recommend specifying ^exact^ whenever samples are
    small.  A conservative rule-of-thumb for 2x2 tables is to specify ^exact^
    when the least-frequent cell contains fewer than 1,000 cases.  Note that
    ^exact^ does not affect whether exact confidence intervals are calculated;
    commands always calculate exact confidence intervals where they can unless
    ^tb^ or ^woolf^ is specified.

^tb^ requests that test-based confidence intervals be calculated wherever approp-
    riate in place of confidence intervals based on other approximations or
    exact confidence intervals.  We recommend that test-based confidence inter-
    vals be used only for pedagogical purposes and never be used for research
    work.

^woolf^ requests that the Woolf approximation, also known as the Taylor expan-
    sion, be used for calculating the standard error of the odds ratio.  Other-
    wise, the Cornfield approximation is used.  The Cornfield approximation
    takes substantially longer (a few seconds) to calculate than the Woolf
    approximation.  


The table for genetic case-control study data is

			     Allele	
			            A    Not_A
		------------+---------------------
		Cases       |       a        b
		Noncases    |       c        d


The basic syntax (ignoring options) for ^gencci^ is "^gencci^ #a #b #c #d".
For example:

	. ^gencci 7 12 9 2^
	. ^gencci 7 12 9 2, exact^
	. ^gencci 7 12 9 2, exact level(90) tb^

The basic syntax (ignoring options) for ^gencc^ is "^gencc^ locus1 locus2,
^group(^case_var^)^".  case_var contains 1 if the observation represents a case
and nonzero (e.g., 1) if it represents a noncase. Frequency weights are
allowed.

	. ^list^
        	    a1         a2        cnt       case 
	  1.         N          N         38          0  
	  2.         M          M         53          0  
	  3.         M          N         95          0  
	  4.         M          M         43          2  
	  5.         N          N         28          2  
	  6.         M          N         85          2  


 	. ^gencc a1 a2 [freq=cnt], group(case)^
	  (output omitted)

If "^[freq=cnt]^" is not specified, each observation contributes 1.

Also see
--------

Manual:  ^[R] epitab [R]symmetry^ 
On-line:  help for @epitab@, @symmetry@, @tabulate@