/*   startup.sas   */;
**********************************************************************
*                                                                    *
*     SASGENE 1.1                                                    *
*     Program for Analysis of                                        *
*     Gene Segregation and Linkage                                   *
*     November 5, 1997                                               *
*                                                                    *
*     Example of Invoking SASGENE macros                             *
*                                                                    *
*********************************************************************;


**********************************************************************
*                                                                    *
* Specify file names and include macros.                             *
*                                                                    *
* 1.  Specify the name of the file where the data is stored.         *
*     The name is enclosed in quotes.                                *
*     example: filename in 'orig.dat' ;                              *
*                                                                    *
* 2.  Include the macros with the %INCLUDE (%inc) statement.         *
*     Specify the physical name of the external file where the macro *
*     is stored.  The physical name is enclosed in quotes.           *
*     example: %inc 'convert.sas';                                   *
*              %inc 'sgene.sas';                                     *
*              %inc 'linkage.sas';                                   *
*                                                                    *
*     Summary:                                                       *
*     The user only needs to change the information inside the       *
*     quotes on the FILENAME and %INCLUDE statements below.          *
*     The information inside the quotes specifies the name of the    *
*     external file where the data or macros are stored.  It may be  *
*     necessary to specify the entire file name inside the quotes.   *
*     example: %inc 'c:\sasmacro\convert.sas';                       *
*********************************************************************;


filename in 'example.dat';  /* name and location of data file    */
%inc 'convert.sas';   /* name and location of SAS macro CONVERT  */
%inc 'sgene.sas';     /* name and location of SAS macro SGENE    */
%inc 'linkage.sas';   /* name and location of SAS macro LINKAGE  */


**********************************************************************
*   include any desired titles and options                           *
*********************************************************************;
title  'Cucumber Gene Linkage Example';
options nodate pageno=1;
options linesize=80 pagesize=500;


**********************************************************************
*   Create SAS dataset                                               *
*     The user will need to modify the INPUT statement to specify    *
*     the gene names from their experiment.  If list input is used,  *
*     then missing values should be coded with a "."                 *
*                                                                    *
*     Macros are expecting the following variable names:             *
*     family = family code                                           *
*     gnr    = generation code                                       *
*                                                                    *
*     Macros are expecting the following values for GNR variable:    *
*      1 for P1                                                      *
*      2 for P2                                                      *
*      3 for F1                                                      *
*      4 for F2                                                      *
*      5 for BC1P1                                                   *
*      6 for BC1P2                                                   *
*                                                                    *
*     P1, P2 and F1 generations must be included                     *
*     for program to run (1 plant each is sufficient)                *
*********************************************************************;
data original;
   infile in missover pad; /* MISSOVER & PAD are options on INFILE */
   input plot rep family gnr plnt bi $ rc $ dv $ sp $ ll $ df $
         f $ b $ d $ u $ tu $ ;
   run;


**********************************************************************
*   Invoke the CONVERT macro if the user needs to convert the gene   *
*   values to "D" or "R".  Otherwise delete the %convert statement.  *
*   The SGENE and LINKAGE macros are expecting the following gene    *
*   values:                                                          *
*    D for Dominant,                                                 *
*    R for Recessive,                                                *
*    . or blank for missing value.                                   *
*                                                                    *
*   Specify the following parameters:                                *
*      DS    - SAS dataset to convert                                *
*      GENES - gene names from the SAS dataset                       *
*      DSOUT - output SAS dataset that has been converted            *
*********************************************************************;
%convert(ds=original,
         genes=BI RC DV SP LL DF F B D U TU,
         dsout=new);


**********************************************************************
*   Invoke the SGENE macro.                                          *
*   Modify the following parameters for your experiment:             *
*      DS    - SAS dataset to analyze (possibly the output dataset   *
*              from the CONVERT macro.                               *
*      GENES - gene names from the SAS dataset                       *
*      P1    - critical value for about half of the frequency of one *
*              parent to determine the expected segregation ratio    *
*              (1:1 or 1:0) in BC1 generation.                       *
*                                                                    *
*              Indicates the number of plants of parent 1            *
*              that you feel must have the trait                     *
*              before you accept it as uniform                       *
*              (for example, 15 plants of P1 measured;               *
*              critical value set at 10,                             *
*              allowing 5 misclassifications)                        *
*********************************************************************;
%sgene(ds=new,
       genes=BI RC DV SP LL DF F B D U TU,
       p1=9
       );


**********************************************************************
*   Invoke the LINKAGE macro.                                        *
*   Modify the following parameters for your experiment:             *
*      DS    - SAS dataset to analyze (possibly the output dataset   *
*              from the CONVERT macro.                               *
*      GENES - gene names from the SAS dataset                       *
*      P1, P2- critical value for about half of the frequency of     *
*              the parents to determine if the phase is coupling or  *
*              repulsion.                                            *
*                                                                    *
*              Indicates the number of plants of parent 1            *
*              that you feel must have the trait                     *
*              before you accept it as uniform                       *
*              (for example, 15 plants of P1 measured;               *
*              critical value set at 10,                             *
*              allowing 5 misclassifications)                        *
*********************************************************************;
%linkage(ds=new,
      genes=BI RC DV SP LL DF F B D U TU,
      p1=9,
      p2=9
      );