PREST (Pedigree RElationship Statistical Test). A program that checks pedigrees for errors. Copyright (C) 2000 Lei Sun, Kenneth Wilder, Mary Sara McPeek Homepage: http://fisher.utstat.toronto.edu/sun/Sotware/Prest Release 1.0. July 22, 2000 1.01 July 25, 2000 2.0 August 10, 2000 2.01 September 05, 2000 2.02 October 30, 2000 2.03 November 28, 2000 3.0 January 10, 2001 3.01 April 30, 2003 3.02 February 15, 2005 =========================================================== License This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY of FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program (see file gpl.txt); if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. We request that use of this software be cited in publications as M.S. McPeek and L. Sun (2000) "Statistical Tests for Detection of Misspecified Relationships by Use of Genome-Screen Data" American Journal of Human Genetics 66:1076-1094. To contact the author: Lei Sun Department of PHS University of Toronto 155 College Street Toronto, ON M5T 3M7 email: sun@utstat.toronto.edu =========================================================== Installation instructions: 1. Download the PREST package. This package includes two programs. One is 'prest.c' (Pedigree RElationship Statistical Test) and the other one is 'altertest.c' (ALTERnative TEST). The two programs can be run independently. The PREST distribution now also includes an R program 'prest.r' written by Daniel E. Weeks that draws out the relationship triangles. 2. Read the files 'Overview', 'Input', 'Output' and 'Tips' carefully to understand the purpose of this program and how it works. 3. Edit the 'Makefile' as necessary according to the instructions in the 'Makefile'. You should only need to make sure that the correct compiler and compiler options for your machine are chosen. 4. Type 'make'. This will build an executable program 'prest'. Type 'make altertest'. This will build an executable program 'altertest'. 5. To run the executable program 'prest': First, prepare the input files, e.g., "ex_pedigrees" and "ex_chromfiles" (see the files 'Example' and 'Input' for more details). Then, I. if use option 1 (perform fast EIBD, AIBS and IBS test only), type prest ex_pedigrees ex_chromfiles 1 II. if use option 2 (also perform MLRT test; this takes substantially more time), type prest ex_pedigrees ex_chromfiles 2 6. To run the executable program 'altertest': First, prepare the input files, e.g., "ex_altertest_input" and "ex_chromfiles" (see the files 'Example' and 'Input' for more details). Then, type altertest ex_altertest_input ex_chromfiles 7. You can test the executable program 'prest' by running it with the sample input files 'ex_pedigrees' and 'ex_chromfiles'. You can then compare your output in the files 'prest_out1', 'prest_out2' and 'prest_out3' with the correct output in the sample output files 'ex_out1_option1', 'ex_out2_option1' and 'ex_out3_option1' (if option 1 were used) or 'ex_out1_option2', 'ex_out2_option2' and 'ex_out3_option2' (if option 2 were used). 8. You can test the executable program 'altertest' by running it with the sample input files 'ex_altertest_input and 'ex_chromfiles'. You can then compare your output in the file 'altertest_out' with the correct output in the sample output file 'ex_altertest_out'. 9. The programs stop if any errors are detected in the format of the input files. Check the output file 'prest_errors' (if you run 'prest') or 'altertest_errors' (if you run 'altertest') for all the errors. 10. Read the file 'About Weeks's R Program' carefully to understand the purpose of the R program 'prest.r'. This program runs fine in Splus as well as in R. To run the program in R or in Splus: > source("prest.r") > postscript(paper="letter",horizontal=F) > prest("prest_out2") > dev.off() The above sequence of commands will read in the 'prest_out2' file and draw out one relationship triangle for each line in the file. The resulting plots will be written to a Postscript file (under R, the default name of this file is "Rplots.ps").