This program computes the likelihood ratio test statistic
as well as the lod score using both the quantitative and qualitative 
phenotypes of the traits for ASP data. 
This program calls genehunter inside the program to compute the IBD sharing
of the ASPs and then using these IBD scores and the associated quantitative traits 
to conduct the LR test.

* Program input files

The input files for the program are: a marker file, a pedigree file, 
a phenotype file, and increment step size, see examples below. 
The first two files are the same as genehunter input files. 
These files are used to run genehunter for computing 
IBD sharings. The increment step size is scan step size for running genehuter, 1 is for 
two point analysis and 2 or more is for multipoint analysis. phenotype file is the data file 
with pedigree information and the quantitative trait values. phenotype file contains 7 
columns: family id, individual id, father id, mothe id, sex, affection status, and the 
associated quantitative trait measurement. Affection status are 1 for unaffected and 2 for 
affected. 

This program is also applicable for data that most families have ASPs and a few  
have more than two afected children.

* How to obtain the program

First, obtain the program from the web site: www/stat.uiowa.edu/~jian.
1. Down load the file "CLR.tar" to your working directory.
2. then type: tar xvf CLR.tar. This will create a directory CLR which contains all the files
   you need to run the program. 

* How to run the program

Compile the program using the commands: make
This creates an excutable code called clr.exe.

To run the program, you can choose one of the following ways:

		(a) type: clr.exe marker.dat ped.dat phe.dat 2
		
		or (b) type: clr.exe then hit return and enter the required file names 
		by typing them on the screen.

* Output results
 
Results are printed in an outer file "results.dat". The program output three columns:
position, -2log(LR), and lod score.

* Parameters for array dimension are defined in file "param.h":

max_pair: maximum number of ASPs, default is 250
max_phenotype: maximum number of observations in phenotype file excluding parents, 
               default is 800
max_ibd_file: maximum observations in genehunter "dump ibd" output siblings only,
              default is 50000
max_pos: maximum number of positions scan in genehunter, default is 300

Note that the maximum id (family id and individal id) length is 10.

* Example files

A sample input files for using the program are included as as a reference for the users.

marker file:

6 0 0 5  << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM 
 0 0.0 0.0 0 << MUT LOCUS, MUT MALE, MUT FEM, HAP FREQ (IF 1) 
1 2 3 4 5 6
1   2  << AFFECTION, NO. OF ALLELES 
0.8000  0.2000 << GENE FREQUENCIES 
1 << NO. OF LIABILITY CLASSES 
0 0  0.5000 << PENETRANCES 
3 8 # 1 
  0.04 0.02 0.08 0.05 0.15 0.46  0.16 0.04
3 8 # 2 
 0.07 0.11 0.21 0.15 0.29 0.12 0.02 0.03
3 10 # 3 
  0.02 0.22 0.02 0.05 0.02 0.02  0.1 0.1 0.05 0.4 
3 8 # 4 
  0.21 0.01 0.01 0.27 0.06 0.03  0.11 0.3
3 11 # 5 
  0.10 0.02 0.03 0.27 0.35 0.09  0.05 0.04 0.01 0.01 0.03
0 0  << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
   0.00  6 12 18 23
1 0.10000 0.48000 << REC VARIED, INCREMENT, FINISHING VALUE 

pedigree file:

 1  1002     0     0 2 2 5 6 1 5 10 10 4 7 2 5
 1  1001     0     0 1 1 4 6 4 6 10 10 4 8 4 4
 1  1003  1001  1002 2 2 4 6 5 6 10 10 4 7 4 5
 1  1004  1001  1002 1 2 5 6 1 4 10 10 4 8 2 4
 2  2001     0     0 1 1 3 6 2 5 8 9 6 8 7 8
 2  2002     0     0 2 2 4 6 5 6 8 9 1 7 1 4
 2  2003  2001  2002 1 2 3 6 2 6 9 9 1 6 1 8
 2  2004  2001  2002 1 2 6 6 5 6 9 9 1 8 4 7
 
quantitative phenotype file:

 1  1002     0     0 2 2 .
 1  1001     0     0 1 1 .
 1  1003  1001  1002 2 2 .
 1  1004  1001  1002 1 2 .
 2  2001     0     0 1 1 723.5
 2  2002     0     0 2 2 380.5
 2  2003  2001  2002 1 2 1985.5
 2  2004  2001  2002 1 2 1985.5

increment step size is a positive integer used for running genehunter.
1--two point linkage analysis; 2 or more for multipoint linkage analysis;
The default value is 5.