debian/0000755000000000000000000000000011673604161007173 5ustar debian/unknown.10000644000000000000000000000343611110210530010735 0ustar .TH UNKNOWN 1 "April 15, 2003" .SH NAME unknown \- identify possible genotypes for unknowns .SH SYNOPSIS A program to rapidly identify which genotypes are possible for individuals typed as unknowns in the input pedigree. .PP .B unknown [ .B -cl ] .SH DESCRIPTION .B unknown infers possible genotypes and mating combinations for parents with unknown genotypes for .IR ilink (1), .IR mlink (1) and .IR linkmap (1). .SH OPTIONS .TP .B \-c Use conditional allele frequencies. .TP .B \-l Choose a good set of loop breakers automatically. .SH "RETURN VALUE" .ta \w'255 'u 0 Successful completion .SH ERRORS .nf .ta \w'255 'u 10 File not found 255 Failure .SH EXAMPLES Normally, .BR unknown (1) is run immediately prior to its sister programs, .IR ilink (1), .IR mlink (1) and .IR linkmap (1), like this: unknown .br mlink .SH FILES .BR unknown (1) reads the two files \fIpedfile.dat\fR and \fIdatafile.dat\fR as its own input and produces various temporary files that are used as input to the next program. These temporary files are \fIipedfile.dat\fR, \fIupedfile.dat\fR, \fIspeedfile.dat\fR and \fInewspeedfile.dat\fR. .SH NOTES .BR unknown (1) is part of the .BR FASTLINK package, which is a re-implementation of the .BR LINKAGE suite of computer tools that help investigate genetic linkage as first proposed G.M. Lathrop, J.M. Lalouel, C. Julier, and J. Ott. .SH AUTHORS Dylan Cooper, Alejandro Schaffer, and Tony Schurtz based on work originally by Jurg Ott, Ph.D, et. al. .PP This manual page was written by Elizabeth Barham for the Debian GNU/Linux system (but may be used by others). .SH WORD-WIDE-WEB http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html .SH "SEE ALSO" .\" Always quote multiple words for .SH .IR ilink (1), .IR linkmap (1), .IR lodscore (1), .IR mlink (1). debian/fastlink.manpages0000644000000000000000000000012211110210530012471 0ustar debian/ilink.1 debian/linkmap.1 debian/lodscore.1 debian/mlink.1 debian/unknown.1 debian/fastlink.html0000644000000000000000000004146611110210530011662 0ustar FASTLINK Home Page
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   Overview

Genetic linkage analysis is a statistical technique used to map genes and find the approximate location of disease genes. There was a standard software package for genetic linkage called LINKAGE. FASTLINK is a significantly modified and improved version of the main programs of LINKAGE that runs much faster sequentially, can run in parallel, allows the user to recover gracefully from a computer crash, and provides abundant new documentation. FASTLINK has been used in over 1000 published genetic linkage studies.

Version 1.0 of FASTLINK was first distributed in May 1993. We are now up to version 4.1P, first released in July 1999. You can download the current version with all documentation as well as some individual documentation files by following the hyperlinks on the left-hand side of this page. When you retrieve FASTLINK as a whole, you will get 1 file called fastlink.tar.Z. To unpack the archive on a UNIX machine, issue the commands 

           uncompress fastlink.tar.Z
           tar -xvf fastlink.tar
Users who do not have access to uncompress and tar equivalents can get the entire distribution piecemeal by ftp'ing to the server fastlink.nih.gov, logging in as user anonymous, and going to the directory pub/fastlink. Start with the file README, which is available by a direct hyperlink on the left to get a roadmap to all the documentation. If you want to see whether a new version of FASTLINK contains improvements that you want, look at the file README.updates, also available by a single click on the left. Thanks to David Stockton executables of the FASTLINK programs suitable for Macintosh OS X are available either by clinking on a hyperlink on this page or from the ftp site fastlink.nih.gov under directory pub/fastlink/mac. Other files of interest to Macintosh users are in that ftp directory.

The FASTLINK project is directed by Alejandro Schäffer. Over the years, participants in developing FASTLINK and providing customer service have included: Richa Agarwala (NIH) Ann Becker (Technion), Robert Cottingham Jr., Alan Cox (Rice U.), Sandhya Dwarkadas (now at U. Rochester), Dan Geiger (Technion), Sandeep Gupta (now at Trilogy), Christopher Hoelscher, Chris Hyams (now at Trilogy), Ramana Idury (now at Kiva Genetics), Peter Keleher (now at U. Maryland), K. Shriram (Rice U.) Willy Zwaenepoel (Rice U.). I am also very grateful to hundreds of users around the world for comments, questions, suggestions, and bug reports, and most of all for being bold enough to try some new software and stick with it.

The FASTLINK project has benefited from two interesting concepts from computer systems. First, K. Shriram implemented a checkpointing facility that allows the FASTLINK main programs to recover gracefully from a crash of the underlying computer. Stephen Rich (now at Wake Forest U.) gets the prize for the most unusual usage of checkpoint/crash recovery. Just before moving his workstation from Minnesota to North Carolina, he killed an ongoing FASTLINK run, and shut down the computer. Once he and the workstation got installed in North Carolina, he resumed the run near where it left off and completed it successfully. I have reused some of K. Shriram's checkpointing code in the PSI-BLAST module of the widely used BLAST package.

Starting with version 2.3P, the ilink, mlink, and linkmap programs in FASTLINK can run in parallel. What is especially surprising is that essentially the same code can run on either shared-memory multiprocessors or on homogeneous networks of uniprocessors. This feat is made possible by using the TreadMarks distributed shared memory system developed at Rice University.

FASTLINK comes with substantial documentation. Most of the documentation files are in ASCII text. Two of the more popular documents that are in PostScript are: The Mystery of (the) Unknown, which explains the preprocessor program unknown, and Loops in FASTLINK . You can download PostScript versions by clicking on the hyperlinks to the left or read the documents one page at a time by clicking on the hyperlinks in this paragraph. Thanks to many users and especially the student participants on the FASTLINK projects who kept asking questions that deserved clear and written answers for everyone's benefit.

To promote better understanding of how to do simple linkage analyses, I teach a class called "Cookbook Linkage Analysis, Ab Initio" . Follow the hyperlink in this paragraph to get to a page that lets you link to the course overheads and 11 recipes for different aspects of linkage analysis. Thanks to Jim Tomlin for putting the course materials on the Web.

I maintain a mailing list of FASTLINK users, used mostly to announce new versions, updates, and bug fixes. If you have retrieved the code and would like to be on the mailing list, send me e-mail at schaffer@helix.nih.gov.

 
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debian/fastlink-doc.doc-base.loops0000644000000000000000000000037311110210530014261 0ustar Document: fastlink-loops Title: Loops in Fastlink Author: Alejandro A. Schäffer Abstract: This document describes some aspects of pedigree loops in fastlink. Section: Science/Biology Format: postscript Files: /usr/share/doc/fastlink-doc/loops.ps.gz debian/fastlink-doc.doc-base.fastlink0000644000000000000000000000065611110210530014744 0ustar Document: fastlink Title: Faster Sequential Genetic Linkage Computations Author: Robert W. Cottingham Jr., Ramana M. Idury, Alejandro A. Schäffer Abstract: This document describes the basics of the fastlink allgorithm which is based on linkage analysis using maximum likelihood estimation which is a powerful tool for locating genes. Section: Science/Biology Format: postscript Files: /usr/share/doc/fastlink-doc/paper1.ps.gz debian/source/0000755000000000000000000000000011514000656010464 5ustar debian/source/format0000644000000000000000000000001411513054733011676 0ustar 3.0 (quilt) debian/fastlink.install0000644000000000000000000000020211673604001012361 0ustar 4.1P/src/lodscore usr/bin 4.1P/src/ilink usr/bin 4.1P/src/linkmap usr/bin 4.1P/src/mlink usr/bin 4.1P/src/unknown usr/bin debian/copyright0000644000000000000000000000257411513776726011150 0ustar X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat X-Debianized-By: Andreas Tille X-Debinized-Date: Wed, 1 Dec 2004 14:19:29 +0100. X-Source-Downloaded-From: ftp://ftp.ncbi.nih.gov/pub/fastlink/fastlink.tar.Z X-Upstream-Author: Alejandro Schaffer X-Homepage: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html Files: * Copyright: (C) 2000-2007 Alejandro Schaffer 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 or 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; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. X-Comment: On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. Files: debian/* Copyright: 2003-2008 Andreas Tille on License: Same as fastlink itself debian/lodscore.10000644000000000000000000000257311115221622011062 0ustar .TH LODSCORE 1 "April 15, 2003" .SH NAME lodscore \- compares likelihoods at locally optimal theta .SH SYNOPSIS .B lodscore .RI [ options ] " ipedfile.dat pedfile.dat" .SH DESCRIPTION This manual page documents briefly the .B lodscore command. In fact this is a very raw intend to provide a manpage because the Debian GNU/Linux distribution requires each program to have a manpage. Any enhancement would be greatly apreciated. .PP \fBlodscore\fP is part of the \fBfastlink\fP software package. .PP .B Lodscore compares -2log(likelihood) at the locally optimal theta to -2log(likelihood) at a theta that is 1/2 in every component (i.e. each locus unlinked to all the rest). In LINKAGE ILINK more likelihood function evaluations are done after the last printed iteration line, but these likelihood function evaluations are unnecessary (see paper2.ps from the .I fastlink-doc Debian package for more details). .SH OPTIONS There might be options but I did not found any information about them. Please foreward any information about them to .SH SEE ALSO ilink(1), linkmap(1), mlink(1), unknown(1). .br .SH Word-Wide-Web: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html .SH AUTHOR: .I Alejandro Schaeffer and others .PP This manual page was written by Andreas Tille , for the Debian GNU/Linux system (but may be used by others). debian/compat0000644000000000000000000000000211673602634010374 0ustar 8 debian/linkmap.10000644000000000000000000000176611110210530010675 0ustar .TH LINKMAP 1 "April 15, 2003" .SH NAME linkmap \- calculates location scores of one locus against a fixed map of other loci .SH SYNOPSIS .B linkmap .RI [ options ] " ipedfile.dat pedfile.dat" .SH DESCRIPTION This manual page documents briefly the .B linkmap command. In fact this is a very raw intend to provide a manpage because the Debian GNU/Linux distribution requires each program to have a manpage. Any enhancement would be greatly apreciated. .PP \fBlinkmap\fP is part of the \fBfastlink\fP software package. .SH OPTIONS There might be options but I did not found any information about them. Please foreward any information about them to .SH SEE ALSO ilink(1), lodscore(1), mlink(1), unknown(1). .br .SH Word-Wide-Web: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html .SH AUTHOR: .I Alejandro Schaeffer and others .PP This manual page was written by Andreas Tille , for the Debian GNU/Linux system (but may be used by others). debian/mlink.10000644000000000000000000000173011110210530010343 0ustar .TH MLINK 1 "April 15, 2003" .SH NAME mlink \- calculates lod scores and risk with two of more loci .SH SYNOPSIS .B mlink .RI [ options ] " ipedfile.dat pedfile.dat" .SH DESCRIPTION This manual page documents briefly the .B mlink command. In fact this is a very raw intend to provide a manpage because the Debian GNU/Linux distribution requires each program to have a manpage. Any enhancement would be greatly apreciated. .PP \fBmlink\fP is part of the \fBfastlink\fP software package. .SH OPTIONS There might be options but I did not found any information about them. Please foreward any information about them to .SH SEE ALSO ilink(1), linkmap(1), lodscore(1), unknown(1). .br .SH Word-Wide-Web: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html .SH AUTHOR: .I Alejandro Schaeffer and others .PP This manual page was written by Andreas Tille , for the Debian GNU/Linux system (but may be used by others). debian/get-orig-source0000644000000000000000000000131711513777766012152 0ustar #!/bin/sh -e NAME=fastlink UPSTREAMTAR="$NAME".tar.Z MAINVERSION="4.1P" mkdir -p ../tarballs cd ../tarballs if [ ! -f "$UPSTREAMTAR" ] ; then wget ftp://ftp.ncbi.nih.gov/pub/fastlink/fastlink.tar.Z fi tar -xzf "$UPSTREAMTAR" PATCHVERSION=`grep -v "^ " fastlink/README.updates | tail -n 1 | sed 's/^\([0-9a-z]\+\)\..*/\1/'` UPSTREAMVERSION="${MAINVERSION}-fix${PATCHVERSION}" UPSTREAMDIR="${NAME}-${UPSTREAMVERSION}" mv "$NAME" "$UPSTREAMDIR" # Remove useless files rm -rf "$UPSTREAMDIR"/aix \ "$UPSTREAMDIR"/4.1P/alphavms \ "$UPSTREAMDIR"/4.1P/irix \ "$UPSTREAMDIR"/4.1P/vaxvms GZIP="--best --no-name" tar -czf "$NAME"_"$UPSTREAMVERSION".orig.tar.gz "$UPSTREAMDIR" rm -rf "$UPSTREAMDIR" debian/fastlink-doc.doc-base.traverse0000644000000000000000000000042311110210530014754 0ustar Document: fastlink-traverse Title: Pedigree Traversal in Fastlink Author: Alejandro A. Schäffer Abstract: This document describes some aspects of pedigree traversal in Fastlink. Section: Science/Biology Format: postscript Files: /usr/share/doc/fastlink-doc/traverse.ps.gz debian/control0000644000000000000000000000474611673604134010611 0ustar Source: fastlink Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille , Charles Plessy Build-Depends: cdbs, debhelper (>= 8) Standards-Version: 3.9.2 Homepage: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/fastlink/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/fastlink/trunk/ Package: fastlink Architecture: any Section: science Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: fastlink-doc Description: faster version of pedigree programs of Linkage Genetic linkage analysis is a statistical technique used to map genes and find the approximate location of disease genes. There was a standard software package for genetic linkage called LINKAGE. FASTLINK is a significantly modified and improved version of the main programs of LINKAGE that runs much faster sequentially, can run in parallel, allows the user to recover gracefully from a computer crash, and provides abundant new documentation. FASTLINK has been used in over 1000 published genetic linkage studies. . This package contains the following programs: ilink: GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions linkmap: calculates location scores of one locus against a fixed map of other loci lodscore: compares likelihoods at locally optimal theta mlink: calculates lod scores and risk with two of more loci unknown: identify possible genotypes for unknowns Package: fastlink-doc Architecture: all Section: doc Depends: ${misc:Depends} Suggests: fastlink Description: Some papers about fastlink Genetic linkage analysis is a statistical technique used to map genes and find the approximate location of disease genes. There was a standard software package for genetic linkage called LINKAGE. FASTLINK is a significantly modified and improved version of the main programs of LINKAGE that runs much faster sequentially, can run in parallel, allows the user to recover gracefully from a computer crash, and provides abundant new documentation. FASTLINK has been used in over 1000 published genetic linkage studies. . You do not really need these papers about fastlink but it is highly recommended to study this documentation before starting with the tools of the fastlink package. debian/README.Debian0000644000000000000000000000125711110210530011214 0ustar fastlink for Debian ---------------------- I uncompressed and untared the downloaded latest archive fastlink.tar.Z, renamed the resulting directory to fastlink-4.1P-fix81 (because of the last bugfix with no. 81), and made a new tarball fastlink-4.1P-fix81.tar.gz which was then used for upgrading the previous Debian package version with uupdate. -- Dr. Guenter Bechly , Sat, 12 May 2001 18:43:26 +0200 I just adopted this procedure in naming the orig.tar.gz file. Moreover I removed some files which are very specific for running fastlink on AIX, VMS and IRIX just to save some disk space. -- Andreas Tille Tue, 15 Apr 2003 09:51:31 +0200 debian/fastlink-doc.doc-base.unknown0000644000000000000000000000046611110210530014627 0ustar Document: fastlink-unknown Title: The Mystery of Unknown Author: Alejandro A. Schäffer Abstract: This document describes some aspects of the UNKNOWN auxiliary program that is distributed with the fastlink package. Section: Science/Biology Format: postscript Files: /usr/share/doc/fastlink-doc/unknown.ps.gz debian/fastlink-doc.doc-base.parallelization20000644000000000000000000000066311110210530016403 0ustar Document: fastlink-parallelization2 Title: Integrating Parallelization Strategies for Linkage Analysis Author: Sandeep K. Gupta, Alejandro A. Schäffer, Alan L. Cox, Sandhya Dwarkadas Abstract: This document describes a second parallel implementation of the ILINK program from the LINKAGE package that improves the previous implementation. Section: Science/Biology Format: postscript Files: /usr/share/doc/fastlink-doc/paper4.ps.gz debian/fastlink-doc.doc-base.avoid-recomp0000644000000000000000000000057011110210530015511 0ustar Document: fastlink-avoid-recomp Title: Avoiding Recomputation in Linkage Analysis Author: Alejandro A. Schäffer, Sandeep K. Gupta, K. Shriram, Robert W. Cottingham Jr. Abstract: This document describes improvements over the original LINKAGE program which were applied in fastlink. Section: Science/Biology Format: postscript Files: /usr/share/doc/fastlink-doc/paper2.ps.gz debian/fastlink-doc.doc-base.parallelization0000644000000000000000000000052411110210530016315 0ustar Document: fastlink-parallelization Title: Parallelization of General Linkage Analysis Problems Author: Sandhya Dwarkadas, Alejandro A. Schäffer, et. all. Abstract: This document describes a parallel implementation of a linkage analysis program. Section: Science/Biology Format: postscript Files: /usr/share/doc/fastlink-doc/paper3.ps.gz debian/fastlink-doc.doc-base.alleles0000644000000000000000000000063211110210530014544 0ustar Document: fastlink-alleles Title: Faster Linkage Analysis Computations for Pedigrees with Loops or Unused Alleles Author: Alejandro A. Schäffer Abstract: This document describes the implementation in FASTLINK of some algorithmic improvements to partly address the problems of pedigree loops and unknown genotypes. Section: Science/Biology Format: postscript Files: /usr/share/doc/fastlink-doc/paper5.ps.gz debian/fastlink-doc.doc-base.random0000644000000000000000000000052511110210530014404 0ustar Document: fastlink-random Title: Random Algorithms for the Loop Cutset Problem Author: Ann Becker, Dan Geiger, Alejandro A. Schäffer Abstract: This document describes how to find a minimum loop cutset in a Bayesian network with high probability. Section: Science/Biology Format: postscript Files: /usr/share/doc/fastlink-doc/paper7.ps.gz debian/datafile.50000644000000000000000000003122011110210530011003 0ustar .TH DATAFILE 5 "April 22, 2003" .SH NAME DATAFILE \- LINKAGE's DATAFILE .SH DESCRIPTION Descriptions of loci and other information are contained in .BR DATAFILE (5). The information in this file is divided into four parts .IP 1. 5 general information on loci and locus order; .IP 2. 5 description of loci; .IP 3. 5 information on recombination; .IP 4. 5 program-specific information. .PP In explaining the structure of .BR DATAFILE (5) we will use two concepts of locus order. The first is the input order, or the order in which the phenotypes corresponding to the loci appear in .BR PEDFILE (5). The second is chromosome order, or the physical order assumed for the loci. The input order is fixed once .BR PEDFILE (5) is created, but the chromosome order can be changed to test various hypotheses. Various parameters such as recombination rates, gene frequencies, penetrances, etc., are specified in the .BR DATAFILE (5). These refer to the initial values of these parameters. The analysis programs can modify some of these values for specific purposes, e.g. maximum likelihood estimation. .SH EXAMPLE Before we attempt to explain the format of various parts of the DATAFILE, it is useful to consider a complete file as an example. The following is the DATAFILE for three sex-linked loci, one of which is Duchenne muscular dystrophy; creatine kinase measurements are available for heterozygote testing in women: 3 0 1 5 << no loci, risk locus, sexlinked (if 1), program code 3 0.001 0.001 0 << mut locus, mut mal, mut fem, hap freq (if 1) 1 3 2 << order of loci 2 2 <<< binary factors, # alleles 5.00000E-01 5.00000E-01 << gene freqs 2 << number of binary factors 1 0 0 1 << allelic codes 2 2 <<< binary factors, # alleles 5.00000E-01 5.00000E-01 << gene freqs 2 << number of binary factors 1 0 0 1 << allelic codes 0 2 <<< quan, # alleles 9.99800E-01 2.00000E-04 << gene freqs 1 << number of traits 1.57000E+00 2.10000E+00 2.10000E+00 << genotype means 5.90000E-02 << variance 2.90000E+00 << multiplier for variance in heterozygotes 0 0 << sex difference (if 1) and interference (if 1) 0.1 0.1 << recombination values 1 0.5 0.5 The last line contains information for the .BR mlink (1) program; this is indicated by the program code 5 on the first line. Other parameters are specified as indicated in the comments following certain lines (indicated by << ). Comments are allowed on some lines for easy interpretation of the file. .SS "Loci and Locus Order" The first two lines of DATAFILE contain information on a variety of parameters, including the number of loci (nlocus), a risk locus (risklocus), sex-linked or autosomal data (sexlink), a mutation locus (mutsys) and mutation rates (mutmale and mutfem ), linkage disequilibrium (disequil ), and a program code (nprogram). The first two lines are followed by a third line giving the chromosome order for the loci. The format is: nlocus risklocus sexlink nprogram mutsys mutmale mutfem disequil (chromosome order) Mutsys and the chromosome order of the loci must begin on new lines; comments can follow at the end of each line. Nprogram is not used by the LINKAGE programs, but is required for interfacing with the shell program LCP. It is used to describe the program for which the file is constructed. LCP can use files constructed for one program as input for a different program. Therefore the datafile is not changed for different programs when using LCP. .TS box center ; c|l. Variable Name Valid Values _ nlocus T{ 1 to maxlocus (as specified by a constant in the programs) T} _ risklocus T{ 0 if risk is not to be calculated T} _ T{ disease locus number (input order) if risk is to be calculated T} _ sexlink T{ 0 for autosomal data T} _ T{ 1 for sex-linked data T} _ nprogram 1 CILINK _ 2 CMAP _ 3 ILINK _ 4 LINKMAP _ 5 MLINK _ 6 LODSCORE _ 7 CLODSCORE _ mutsys T{ 0 if mutation rates are zero T} _ T{ mutation locus number (input order) for non-zero mutation rates T} _ mutmale male mutation rate _ mutfem female mutation rate _ disequil T{ 0 if loci are assumed to be in linkage equilibrium T} _ T{ 1 if loci are in linkage disequilibrium T} .TE When loci are in linkage equilibrium, allele frequencies must be given under each locus description; otherwise, haplotype frequencies are provided. When risk is calculated, a disease allele is provided in the locus description for the "risklocus." As an example, consider the analysis of 3 autosomal loci in the chromosome order 1 3 2. The first three lines of the DATAFILE could be: 3 0 0 3 << no loci, risk locus, sexlinked (if 1), program code 3 0.1 0.1 0 << mut locus, mut mal, mut fem, haplotype freq (if 1) 1 3 2 << order of loci The data are autosomal with mutation at the third locus. .SS "Description of Loci" The loci are described in the order in which they appear in the .BR PEDFILE (5). Assuming linkage equilibrium, the gene frequencies are specified as part of the locus description (linkage disequilibrium will be documented in a later version). The descriptions differ according to the type of locus. A numeric code distinguishes each of the types: .TS box center; n|l. 0 Quantitative variable _ 1 Affection status _ 2 Binary factors _ 3 Numbered alleles .TE The format for each locus type, assuming linkage equilibrium, is as follows: .SS "Numbered alleles" The locus description consists of two lines. The first gives the code for numbered alleles and the total number of alleles. The second gives the gene frequencies. For example: 3 2 << numbered alleles code, total number of alleles 0.5 0.5 << gene frequencies specifies two alleles with equal gene frequencies. .SS "Binary factors" The first two lines are similar to those in the previous example. After this the number of factors is specified on a separate line, followed by one line for each allele specification. As an example, consider the case of a recessive trait: 2 2 << binary factor code, number of alleles 0.999 0.001 << gene frequencies 2 << number of factors 1 1 0 1 << alleles .SS "Affection status" The number of liability classes replaces the number of factors, and penetrances are given for each genotype in each class: 1 2 << affection status code, number of alleles 0.999 0.001 << gene frequencies 1 << number of liability classes 0.0 1.0 1.0 << penetrances describes a fully penetrant, dominant disease locus. The genotypes are in the order 11, 12, 22 where 1 is the first allele and 2 is the second allele specified in the gene frequency list. For three alleles, the genotype order is 11, 12, 13, 22, 23, 33. The same pattern is followed for more alleles. To describe a similar locus, but with reduced penetrance and two liability classes, use the following: 1 2 << affection status code, number of alleles 0.999 0.001 << gene frequencies 2 << number of liability classes 0.0 0.5 0.5 0.0 0.9 0.9 << penetrances With sex-linked data, male penetrances must also be defined for each allele. The following describes a sex-linked disease with 50% penetrance in males: 1 2 << affection status code, number of alleles 0.999 0.001 << gene frequencies 1 << number of liability classes 0.0 0.0 1.0 0.0 0.5 << female followed by male penetrances .SS "Quantitative trait" Quantitative traits are described by a first line containing the quantitative code (0) and the number of alleles, and a second line with gene frequencies, as in the previous examples. These are followed by lines indicating the number of quantitative variables, genotypic means for each variable, a variance-covariance matrix, and a constant that gives the ratio of variance-covariance in heterozygotes to homozygotes. For a single quantitative variable, the format is: 0 2 << quantitative variable code, number of alleles 0.999 0.001 << gene frequencies 1 << number of quantitative variables 10.0 12.0 14.0 << genotypic means 1.5 << variance 1.0 << multiplier for heterozygote variance The genotypes are 1/1, 1/2 and 2/2, respectively, where allele 1 has the frequency 0.999. For two quantitative variables, the description is: 0 2 << quantitative variable code, number of alleles 0.999 0.001 << gene frequencies 2 << number of liability classes 10.0 12.0 14.0 -10.0 0.0 10.0 << genotypic means 1.5 10.0 100.0 << variance-covariance 1.0 << multiplier for heterozyg. variance-covariance Only the upper triangle of the variance-covariance matrix is given; the order is V11, V12, V13 ... V22, V23 ... etc. Here, the variance of the first variable is 1.5, the covariance is 10.0, and the variance of the second variable is 100.0. When describing the "risk locus," the disease allele (risk allele) must be designated at the end of the locus description. For example: 1 2 << affection status code, number of alleles 0.999 0.001 << gene frequencies 1 << number of liability classes 0.0 1.0 1.0 << penetrances 2 << risk allele .SS "Recombination Information" In addition to recombination rates, sex-differences and interference must be specified in this section. Sex-difference options are indicated by an integer variable that takes the following values: .TS box center; n|l. 0 T{ no sex-difference T} _ 1 T{ constant sex-difference (the ratio of female/male genetic distance is the same in all intervals) T} _ 2 T{ variable sex-difference (the female/male distance ratio can be different in each interval) T} .TE The interference option can take the following values: .TS box center; n|l. 0 T{ no interference T} _ 1 T{ interference without a mapping function T} _ 2 T{ user-specified mapping function T} .TE Interference (i.e. options 1 or 2) is allowed only in some analysis programs with three loci. The programs, as distributed, contain Kosambi interference as the user-specified mapping function. First, consider a case without interference. When the sex-difference is "0," one recombination rate is given for each of the nlocus-1 segments (see the complete example above). If the sex-difference option is "1," the male recombination rates are given on one line, and the female/male genetic distance is specified on the next line, e.g.: 1 0 << sex difference, interference 0.1 0.2 0.1 << male recombination 2.0 << female/male ratio of genetic distance When the sex-difference option is "2", the male recombination rates are followed on the next line by female recombination rates: 2 0 << sex difference, interference 0.1 0.2 0.1 << male recombination 0.2 0.1 0.2 << female recombination Interference can be specified for three loci. With the interference option 1, three recombination rates are given. These are the recombination rates between adjacent loci in the two segments and the recombination rate between the flanking loci. An example is: 1 1 << sex difference, interference 0.1 0.1 0.18 << male recombination 2.0 << female/male ratio of genetic distance With the interference option 2, only the rates between the adjacent loci are provided: 1 2 << sex difference, interference 0.1 0.1 << male recombination 2.0 << female/male ratio of genetic distance .SS "Program-specific information" The program-specific information consists of a series of lines at the end of the .BR DATAFILE (1) describing which parameters should be varied iteratively by the analysis programs. .SH NOTES The information contained herein was gleaned, often-times verbatim, from .UR http://linkage.rockefeller.edu/soft/linkage/ the LINKAGE User's Guide .UE on the web by kind permission of Jurg Ott, Ph.D. .SH AUTHORS Mark Lathrop and Jurg Ott. .PP This manual page was written by Elizabeth Barham for the Debian GNU/Linux distribution. .SH WORLD-WIDE-WEB .UR http://linkage.rockefeller.edu/soft/linkage/ http://linkage.rockefeller.edu/soft/linkage/ .UE .SH SEE ALSO .BR LINKAGE (5), .BR PEDFILE (5), .BR ilink (1), .BR linkmap (1), .BR lodscore (1), .BR mlink (1), and .BR unknown (1). debian/ilink.10000644000000000000000000000512011110210530010334 0ustar .TH ILINK 1 "April 15, 2003" .SH NAME ilink \- GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions .SH SYNOPSIS .B ilink .RI [ options ] " ipedfile.dat pedfile.dat" .SH DESCRIPTION This manual page documents briefly the .B ilink command. In fact this is a very raw intend to provide a manpage because the Debian GNU/Linux distribution requires each program to have a manpage. Any enhancement would be greatly apreciated. .PP \fBilink\fP is part of the \fBfastlink\fP software package. .PP ILINK uses the GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions. If you use the default scripts produced by lcp, your initial guess for theta is .1 in every dimension. GEMINI evaluates each theta by its likelihood, seeking to find theta vectors that have a higher pedigree likelihood. .PP The GEMINI procedure has multiple iterations. Each iteration corresponds to one line of output. Each iteration includes multiple likelihood function evaluations. Each iteration has two phases. In Phase I GEMINI seeks to improve the current best theta. In Phase II, GEMINI estimates the gradient of the likelihood with respect to the current best theta vector. In the first iteration, Phase I only evaluates the likelihood at the initial candidate theta. When ILINK prints out a line such as: maxcensor can be reduced to -32767, it has completed the first likelihood function evaluation. On long runs, this fact can be used to estimate running time. A reasonable rough estimate for the number of function evaluations is 10*(number of dimensions of theta vector). The number of dimensions of the theta vector is one fewer than the number of loci in most cases. If maletheta and femaletheta are allowed to differ (sexdif is set to 1), then the number of dimensions doubles to 2 * (number of loci - 1). Estimating other parameters (with fitmodel set to true) can also increase the number of dimensions. To learn more about .B ilink it might be useful to read the file .I /usr/share/doc/fastlink/README.ILINK if you have a Debian GNU/Linux system. .SH OPTIONS There might be options but I did not found any information about them. Please foreward any information about them to .SH SEE ALSO linkmap(1), lodscore(1), mlink(1), unknown(1). .br .SH Word-Wide-Web: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html .SH AUTHOR: .I Alejandro Schaeffer and others .PP This manual page was written by Andreas Tille , for the Debian GNU/Linux system (but may be used by others). debian/menu0000644000000000000000000000204011673602265010061 0ustar ?package(fastlink):needs="text" section="Applications/Science/Biology"\ title="Fastlink GEMINI optimization" command="/usr/bin/ilink" \ hints="GEMINI optimization procedure to find a locally optimal value of the theta vector of recombination fractions" ?package(fastlink):needs="text" section="Applications/Science/Biology"\ title="Fastlink location scores" command="/usr/bin/linkmap" \ hints="Calculates location scores of one locus against a fixed map of other loci" ?package(fastlink):needs="text" section="Applications/Science/Biology"\ title="Fastlink compare likelihoods" command="/usr/bin/lodscore" \ hints="Compares likelihoods at locally optimal theta " ?package(fastlink):needs="text" section="Applications/Science/Biology"\ title="Fastlink lod scores" command="/usr/bin/mlink" \ hints="Calculate lod scores and risk with two of more loci" ?package(fastlink):needs="text" section="Applications/Science/Biology"\ title="Fastlink identify genotypes" command="/usr/bin/unknown" \ hints="Identify possible genotypes for unknowns" debian/changelog0000644000000000000000000001516511673604161011055 0ustar fastlink (4.1P-fix95-3) unstable; urgency=low * Replaced debian/*.desktop by debian/menu to make sure users of modern desktop systems using freedesktop.org standards will not be confused by a missing graphical interface Closes: #639998 * debian/control: - Standards-Version: 3.9.2 (no changes needed) - Fixed Vcs fields - Dropped article in short description * Debhelper 8 (control+compat) -- Andreas Tille Mon, 19 Dec 2011 10:34:20 +0100 fastlink (4.1P-fix95-2) unstable; urgency=low * debian/copyright: Fixed source download location * debian/control: - Standards-Version: 3.9.1 - Fix spelling of Debian Med - debhelper (>= 7) - Depends: ${misc:Depends} * debian/compat: 7 * debian/watch: use GZIP="--best --no-name" to make sure the resulting tarball will be identically * debian/source/format: 3.0 (quilt) * debian/rules: remove dh_desktop call -- Andreas Tille Fri, 14 Jan 2011 08:40:14 +0100 fastlink (4.1P-fix95-1) unstable; urgency=low * New upstream bugfix release * debian/control: Better description * Standards-Version: 3.8.0 (no changes needed) * Removed explicite versioning from cdbs and debhelper * Machine readable copyright files * debian/loadscore.1: s?\.5?1/2? because man treated .5 as control * gcc3.3 patch is not needd any more - so neither the quilt dependency is needed -- Andreas Tille Tue, 09 Dec 2008 07:40:11 +0100 fastlink (4.1P-fix94b-2) unstable; urgency=low * Changed the doc-base section according to the new policy. * Added myself to the `Uploaders' field in debian/control. -- Charles Plessy Sun, 06 Jul 2008 22:49:23 +0900 fastlink (4.1P-fix94b-1) unstable; urgency=low * New upstream patch * Don't autogenerate debian/control, remove debian/control.in * Build-Depends: quilt * Standards-Version: 3.7.3 (No changes needed) * debian/control: XCBS-URL -> Homepage * Removed XB-Tag (isn't used) and Homepage from long description * Removed [Biology] from short description * Group maintenance - Maintainer: Debian-Med Packaging Team - DM-Upload-Allowed: yes - Uploaders: Andreas Tille - Vcs-Browser, Vcs-Svn * Doc package to section doc -- Andreas Tille Mon, 18 Feb 2008 17:54:17 +0100 fastlink (4.1P-fix92-1) unstable; urgency=low * New upstream fix package * Standards-Version: 3.7.2 (no changes necessary) * Switched to cdbs * Setting DebTags * Added desktop files -- Andreas Tille Sat, 9 Sep 2006 12:52:33 +0200 fastlink (4.1P-fix91-1) unstable; urgency=low * New bugfix release * removed some files which are very specific for running fastlink on AIX, VMS and IRIX from source package which had to be repackaged anyway. * Standards-Version: 3.6.1.1 -- Andreas Tille Wed, 1 Dec 2004 14:19:29 +0100 fastlink (4.1P-fix88-3) unstable; urgency=low * Fixed maintainer address in debian/control closes: #195322 * Patched 4.1P/src/{commondefs,unknown}.h to replace varargs.h by stdarg.h Ported functions in iostuff.c to get rid of va_* stuff. Many thanks to Colin Watson for his patches. Replaced by These points fix FTBFS with gcc-3.3. closes: #194913 -- Andreas Tille Mon, 2 Jun 2003 09:27:22 +0200 fastlink (4.1P-fix88-2) unstable; urgency=low * What difference does it make to the dead, the orphans and the homeless, whether the mad destruction is wrought under the name of totalitarianism or the holy name of liberty or democracy? -- Mahatma Gandhi (1869 - 1948), "Non-Violence in Peace and War" * Added manpages for data formats and replaced unknown.1. These pages were kindly provided by Elizabeth Barham * fastlink-doc now only suggests fastlink * Added doc-base entries. * CHanged compile time option from -g to -Wall -- Andreas Tille Sat, 26 Apr 2003 13:50:38 +0200 fastlink (4.1P-fix88-1) unstable; urgency=low * The "I'm against war" release Mankind must put an end to war before war puts an end to mankind. -- John F. Kennedy * New upstream release (bugfixes) * New maintainer closes: #100221 * Build-Depends: debhelper (>= 4.0) * Standards-Version: 3.5.9 * debian/compat now stores debhelper compatibility version * Compliant to developers reference "6.3.2. Upstream home page" and XBCS-URL: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html * Updated fastlink.html from web page * Wrote manpages. * Removed the following files from binary package because they just describe Infromation for compilation and installation: README.AIX README.ALPHAVMS README.DOS README.Digital README.IRIX README.VAX README.VMS README.djgpp README.install README.makefile README.portability * Split up into two packages to remove papers from the binary package. This reduces space on Debian mirrors because the main part of the binary package was architecture "all" and probably saves disk space for local installs were these docs are not needed. -- Andreas Tille Tue, 15 Apr 2003 09:51:31 +0200 fastlink (4.1P-fix81-2) unstable; urgency=low * Maintainer set to Debian QA Group . -- Adrian Bunk Fri, 24 Aug 2001 23:06:48 +0200 fastlink (4.1P-fix81-1) unstable; urgency=low * New upstream release (upstream used the same version number 4.1P, but introduced some new bugfixes incl. 78-81); closes: #43471 * Enclosed the fastlink homepage to docs, and a README.Debian. * Updated Debian package internals. -- Dr. Guenter Bechly Sat, 12 May 2001 18:43:26 +0200 fastlink (4.1P-2) unstable; urgency=low * Adopted by new maintainer; closes: #92804 * Removed several unnecessary files in debian subdirectory. * Updated to latest standards version and added Build-Depends (changed control, copyright, dirs, docs, and rules); closes: #91154, #91441, #42712 * Moved package from misc to section science, because it is a tool that is exclusively useful for biologists. -- Dr. Guenter Bechly Sat, 21 Apr 2001 09:17:46 +0200 fastlink (4.1P-1) unstable; urgency=low * New upstream release -- Stephane Bortzmeyer Mon, 19 Jul 1999 17:39:24 +0200 fastlink (4.0P-1) unstable; urgency=low * Initial Release. -- Stephane Bortzmeyer Fri, 5 Feb 1999 15:36:21 +0100 Local variables: mode: debian-changelog End: debian/fastlink-doc.doc-base.autoselect0000644000000000000000000000064711110210530015301 0ustar Document: fastlink-autoselect Title: Automatic Selection of Loop Breakers for Genetic Linkage Analysis Author: Ann Becker, Dan Geiger, Alejandro A. Schäffer Abstract: This document describes how the LINKAGE program was enhanced by an automated process of selecting loop breakers by an hybrid algorithm in the FASTLINK program. Section: Science/Biology Format: postscript Files: /usr/share/doc/fastlink-doc/paper6.ps.gz debian/linkage.50000644000000000000000000001720111110210530010647 0ustar .TH LINKAGE 5 "April 22, 2003" .SH NAME LINKAGE \- general information about LINKAGE's file formats .SH "DESCRIPTION" The input data consist of pedigree and genotypic information contained in one file, and locus descriptions, recombination rates and locus order contained in a second file. These files are entitled .BR PEDFILE (5) and .BR DATAFILE (5), respectivly. .SS "Phenotypes and Genotypes" To understand the format of the input files, you must know what kinds of phenotypic data can be interpreted by the LINKAGE programs. Phenotype data can be one of the following types: .IP \(bu 5 .BR "Numbered alleles". These are codominant alleles at a single locus. The numbers run consecutively from 1 to the maximum number of alleles observed. The phenotype consists of two allele numbers corresponding to a genotype. An unknown genotype is coded as 0 0. .IP \(bu 5 .BR "Binary factors". In this coding scheme a series of binary codes (1 or 0) indicates the presence or absence of a phenotype factor. This system is useful for describing either codominant or recessive/dominant systems. The phenotype is entered as a binary string. .IP \(bu 5 .BR "Affection status". The presence or absence of disease (or other qualitative phenotypes) is described by a numbered code. A risk or liability class can also be included as a separate numeric code. .IP \(bu 5 .BR "Quantitative traits". One or more quantitative measurements can be used as a phenotype description. .PP The phenotypic codes for each of these types of data are described in more detail below. .TP .BR "NOTE": The present version of LINKAGE does not allow mixtures of affection status and quantitative variables, except in the case of sex-linked traits as described below. A future version will incorporate a modification allowing such mixtures for autosomal data. .SS "Numbered Allies" Numbering alleles is the simplest way to code codominant marker data. A homozygote is indicated by repeating the allele number; thus 1 2 indicates that the alleles are 1 and 2 (a heterozygotea) while 1 1 indicates the alleles are 1 and 1 (a homozygote). An unknown genotype is coded as 0 0. For sex-linked loci, males have a single allele. With the allele 1, for example, the phenotype can be coded 1 0 or 1 1. .SS "Binary Factors" Binary factors (sometimes called "factor-union" notation) can also represent phenotypes for codominant marker data, but this coding is most useful with recessive alleles or with complex systems such as Rh, ABO, and Gm. Each allele is assigned a set of properties, called factors, in such a way that all phenotypes can be specified as the union of two allele sets. For codominant loci, each allele can be associated with one factor. If n alleles are present, the ith allele is represented by a series of n binary codes with a 0 in all locations, except in the ith position, which contains a 1. For example, in a two allele system the allelic codes are: .TS center; n1 n1 l. 1 0 (allele 1) 0 1 (allele 2) .TE The three possible phenotypes are: .TS center; n1 n1 l. 1 0 (union of alleles 1 and 1) 1 1 (union of alleles 1 and 2) 0 1 (union of alleles 2 and 2) .TE An unknown phenotype is coded as 0 0. Spaces between the codes are very important; they must be included when entering the phenotypes into the pedigree file as described below. A locus with three codominant alleles is coded as: .TS center; n1 n1 n1 l. 1 0 0 (allele 1) 0 1 0 (allele 2) 0 0 1 (allele 3) .TE The six possible phenotypes are: .TS center; n1 n1 n1 l. 1 0 0 (union of alleles 1 and 1) 1 1 0 (union of alleles 1 and 2) 1 0 1 (union of alleles 1 and 3) 0 1 0 (union of alleles 2 and 2) 0 1 1 (union of alleles 2 and 3) 0 0 1 (union of alleles 3 and 3) .TE and an unknown phenotype is 0 0 0. The advantage of the binary factor coding scheme is evident when a recessive disease gene is under study. To code such a system, we could indicate the normal gene by the presence of a single factor (1) and the disease gene by the absence of this factor (0). The phenotype 1 (unaffected) now corresponds to two possible genotypes, either the union of allele 1 and allele 1 (noncarrier) or the union of allele 1 and allele 0 (carrier). This simple coding is usually not sufficient because both homozygote recessive and unknown phenotypes are coded as 0. To account for this, we introduce a second factor for which a 1 indicates that the phenotype is known, and a 0 that the phenotype is unknown. The allelic codes are: .TS center; n1 n1 l. 1 1 (allele 1) 0 1 (allele 2) .TE and the possible phenotypes are: .TS center; n1 n1 l. 1 1 (union of alleles 1 and 1, or alleles 1 and 2) 0 1 (union of alleles 2 and 2) 0 0 (unknown) .TE .SS "Affected Status" "Affection status" refers to the presence or absence of disease. The programs assume that an affected individual will have the phenotype code "2" and that an unknown individual will have the code "0." By convention, "1" is used to designate unaffected status (in fact, this code can be any integer value other than 0 and 2). If necessary, the unknown and affected codes can be changed in the program code, and the programs recompiled. For an "affection-status" locus, each genotype has an associated penetrance; this is the probability that an individual with a particular genotype will be affected. Penetrance can also be defined as a function of liability classes. In this case, one penetrance is given for each genotype in each liability class. The classes are numbered sequentially starting from 1. With two or more liability classes, the phenotype is the affection status plus the class number. When a single affection status class is defined, the class number is not included as part of the phenotype. With sex-linked traits, different penetrances must be given for females and males. One penetrance in males is specified for each allele in each liability class. .SS "Quantitative Variables" Phenotypic information is sometimes presented in the form of quantitative measurements, e.g. creatine kinase for carrier detection in Duchenne muscular dystrophy. The phenotype is then the quantitative value. Unknown phenotypes are entered as 0.0. (The code for unknown quantitative values is a program constant that can be changed.) The genotypic means, the variance of the trait in homozygotes, and the ratio of the variances in heterozygotes and homozygotes must be specified. If several traits are measured for the same locus, the phenotype is the list of all the variables. A single value of 0.0 in the list is interpreted as an unknown phenotype. The means must be given for each variable as a function of genotype, along with the variance-covariance matrix. The variance matrices for homozygotes and heterozygotes can differ by a constant factor. For sex-linked traits it is assumed that males will have an affection-status variable rather than a quantitative value. If several variables have been measured (ntrait), a male phenotype consists of affection status followed by ntrait-1 arbitrary entries (for example, zeros). The present version of the programs supports only one affection status class, with full penetrance of the disease allele for sex-linked traits. .SH NOTES The information contained herein was gleaned, often-times verbatim, from .UR http://linkage.rockefeller.edu/soft/linkage/ the LINKAGE User's Guide .UE on the web by kind permission of Jurg Ott, Ph.D. .SH AUTHORS Mark Lathrop and Jurg Ott. .PP This manual page was written by Elizabeth Barham for the Debian GNU/Linux distribution. .SH WORLD-WIDE-WEB .UR http://linkage.rockefeller.edu/soft/linkage/ http://linkage.rockefeller.edu/soft/linkage/ .UE .SH SEE ALSO .BR DATAFILE (5), .BR PEDFILE (5), .BR ilink (1), .BR linkmap (1), .BR lodscore (1), .BR mlink (1), and .BR unknown (1). debian/fastlink.docs0000644000000000000000000000041111110210530011627 0ustar README README.ILINK README.Linux README.TreadMarks README.allele README.bugreport README.checkpoint README.constants README.mapfun README.memory README.p4 README.parallel README.scaling README.time README.trouble README.unknown README.updates debian/fastlink.html debian/rules0000755000000000000000000000117611514001635010247 0ustar #!/usr/bin/make -f # debian/rules for fastlink using cdbs # Andreas Tille , GPL # include /usr/share/cdbs/1/rules/patchsys-quilt.mk include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/makefile.mk clean:: cd 4.1P/src; make allclean # Use makefile in subdir DEB_MAKE_INVOKE = cd 4.1P/src; $(DEB_MAKE_ENVVARS) make $(if $(DEB_MAKE_MAKEFILE), -f $(DEB_MAKE_MAKEFILE),) -C $(DEB_BUILDDIR) CFLAGS=$(if $(CFLAGS_$(cdbs_curpkg)),"$(CFLAGS_$(cdbs_curpkg))","$(CFLAGS)") CXXFLAGS=$(if $(CXXFLAGS_$(cdbs_curpkg)),"$(CXXFLAGS_$(cdbs_curpkg))","$(CXXFLAGS)") get-orig-source: sh debian/get-orig-source debian/fastlink-doc.docs0000644000000000000000000000000511110210530012371 0ustar *.ps debian/pedfile.50000644000000000000000000002615411110210530010654 0ustar .TH PEDFILE 5 "April 22, 2003" .SH NAME PEDFILE \- LINKAGE's PEDFILE, Pedigree Information .SH DESCRIPTION In addition to phenotypes and description of loci, the LINKAGE programs require pedigree information in order to traverse the pedigree when calculating the likelihood. The input must contain the following information for each individual: .IP \(bu 5 a pedigree number .IP \(bu 5 an individual identification number, or id .IP \(bu 5 father's id number .IP \(bu 5 mother's id number .IP \(bu 5 first offspring id number .IP \(bu 5 next paternal sibling id number .IP \(bu 5 next maternal sibling id number .IP \(bu 5 sex .IP \(bu 5 "proband status" .PP The first offspring can be any of an individual's children, but the next sib id's for the offspring will be constrained by this choice. The next-paternal-sibling and next-maternal-sibling numbers, along with first-offspring number, provide a set of pointers to pass from one child to the next. The first offspring of the father is any of his children; the next paternal sib of the first offspring is any other of his children, etc. The entry for the next paternal sib of the last child is "0". Similar pointers are made for the mother's children. For full-sibs, it is convenient to make id's for the next maternal and next paternal siblings identical, but when one or both parents have children from different marriages, at least some will have different values. Father and mother id's are 0 for founders, or other members of the pedigree for whom information on parents is absent. Otherwise, both parents must be present in the pedigree even if one is unknown. If one parent is unknown, an id number must still be created, and a record for the fictitious parent must appear in the pedigree file. The "proband" refers to a starting individual for linkage calculations (indicated by a 1 in the proband field). The choice of the proband is not necessarily related to the ascertainment of the pedigree; indeed, it is usually more efficient to calculate from a founding ancestor rather than from the true proband. Risks are also calculated for the person designated as the proband. Other individuals should have a 0 in the proband field, except in pedigrees containing inbreeding or marriage loops as discussed in section 2.8. If no proband is designated, the first individual encountered for a pedigree will be used as a starting point for the calculation. The sex field is coded 1 for males and 2 for females. These default values can be changed by modifying a program constant. The creation of the first offspring, next maternal sib and next paternal sib pointers is done automatically by the program MAKEPED (not covered in this document). The input to the MAKEPED program is a file with individual records containing the pedigree number, id number, father id, mother id, sex and phenotypic data. The phenotypic data are coded as discussed in .BR LINKAGE (5) and in the following examples. The MAKEPED program also allows automatic selection of probands for efficient likelihood calculations. .SH EXAMPLE Consider the pedigree shown in Figure 1. Data on three loci are presented: one disease locus and two marker loci. An "a" below an individual stands for "affected," and "u" stands for unknown. The first marker locus has three alleles present in the pedigree, while the second has two alleles present. [1]--.--(2) a | 22 | 12 12 | 12 Figure 1 | .------+------. | | | (6)--.--[3] [4] (5) | a 13 | 12 12 | 22 | .-------. | | [7] (8)--.--(10) a | 13 u | 12 22 u | 12 | (9) a 11 12 The input PEDFILE can take the following form: .TS center; n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 l l. 1 1 0 0 3 0 0 1 1 2 0 1 0 1 1 Ped: 1 Per: 1 1 2 0 0 3 0 0 2 0 1 1 1 0 1 1 Ped: 1 Per: 2 1 3 1 2 7 4 4 1 0 2 1 1 0 0 1 Ped: 1 Per: 3 1 4 1 2 0 5 5 1 0 1 0 1 0 1 1 Ped: 1 Per: 4 1 5 1 2 0 0 0 2 0 2 1 1 0 0 1 Ped: 1 Per: 5 1 6 0 0 7 0 0 2 0 1 1 0 1 1 1 Ped: 1 Per: 6 1 7 3 6 0 8 8 1 0 2 1 0 1 0 1 Ped: 1 Per: 7 1 8 3 6 9 0 0 1 0 1 0 0 0 0 0 Ped: 1 Per: 8 1 9 8 10 0 0 0 2 0 2 1 0 0 1 1 Ped: 1 Per: 9 1 10 0 0 9 0 0 2 0 1 1 1 0 1 1 Ped: 1 Per: 10 .TE The PEDFILE has been produced from an input file by the MAKEPED program. The comments at the end of each record indicate original pedigree and id codes. The first entry in each record is followed by the pedigree number, id number, five pedigree pointers (father id, mother id, first offspring id, next paternal sib id, next maternal sib id), sex, proband, disease status, and marker loci coded as binary factors. Comparison with the original pedigree will reveal the coding scheme. Individual 1 has been chosen as the "proband;" as this is the first individual of this pedigree encountered in the file, the entry in the proband field is optional. Now consider the same pedigree extended to include some half sibs (Figure 2). [1]--.--(2) a | Figure 2 22 | 12 12 | 12 | .------+------. | | | (6)--.--[3] [4] (5) | a a 13 | 12 22 12 12 | 22 12 22 | .-------------------------. | | (11)--.--[7]--.--(12)--.--[13] (8)--.--(10) | a | | | u | 13 | 12 | u u | 12 u | 22 | 12 | u u | 12 | | | | (14) (15) (16) (9) a 13 13 11 11 12 12 12 12 The MAKEPED program produces the following file for this pedigree (figure 2): .TS center; n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 l l. 1 1 0 0 3 0 0 1 1 2 0 1 0 1 1 Ped: 1 Per: 1 1 2 0 0 3 0 0 2 0 1 1 1 0 1 1 Ped: 1 Per: 2 1 3 1 2 7 4 4 1 0 2 1 1 0 0 1 Ped: 1 Per: 3 1 4 1 2 0 5 5 1 0 1 0 1 0 1 1 Ped: 1 Per: 4 1 5 1 2 0 0 0 2 0 2 1 1 0 0 1 Ped: 1 Per: 5 1 6 0 0 7 0 0 2 0 1 1 0 1 1 1 Ped: 1 Per: 6 1 7 3 6 14 8 8 1 0 2 1 0 1 0 1 Ped: 1 Per: 7 1 8 3 6 9 0 0 1 0 1 0 0 0 0 0 Ped: 1 Per: 8 1 9 8 10 0 0 0 2 0 2 1 0 0 1 1 Ped: 1 Per: 9 1 10 0 0 9 0 0 2 0 1 1 1 0 1 1 Ped: 1 Per: 10 1 11 0 0 14 0 0 2 0 1 0 0 0 0 0 Ped: 1 Per: 11 1 12 0 0 15 0 0 2 0 1 1 1 0 1 1 Ped: 1 Per: 12 1 13 0 0 16 0 0 1 0 1 0 0 0 0 0 Ped: 1 Per: 13 1 14 7 11 0 15 0 2 0 1 1 0 1 1 1 Ped: 1 Per: 14 1 15 7 12 0 0 16 2 0 1 1 0 1 1 1 Ped: 1 Per: 15 1 16 13 12 0 0 0 2 0 1 1 0 0 1 1 Ped: 1 Per: 16 .TE The following data refer to a larger pedigree, taken from a coronary heart disease study, in PEDFILE form: .TS center; n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 n2 l l. 1 1 0 0 3 0 0 2 0 2 3 0 0 0.00 Ped: 1 Per: 1 1 2 0 0 3 0 0 1 1 2 3 0 0 0.00 Ped: 1 Per: 2 1 3 2 1 7 5 5 1 0 2 2 0 0 0.00 Ped: 1 Per: 3 1 4 0 0 7 0 0 2 0 1 2 0 0 0.00 Ped: 1 Per: 4 1 5 2 1 21 0 0 2 0 1 3 0 1 22.70 Ped: 1 Per: 5 1 6 0 0 21 0 0 1 0 2 3 0 0 0.00 Ped: 1 Per: 6 1 7 3 4 26 9 9 1 0 2 2 0 0 0.00 Ped: 1 Per: 7 1 8 0 0 26 0 0 2 0 1 2 0 1 9.20 Ped: 1 Per: 8 1 9 3 4 31 11 11 1 0 2 2 1 1 24.30 Ped: 1 Per: 9 1 10 0 0 31 0 0 2 0 1 2 1 0 9.30 Ped: 1 Per: 10 1 11 3 4 0 12 12 1 0 2 2 1 1 23.90 Ped: 1 Per: 11 1 12 3 4 34 14 14 1 0 2 2 1 1 20.70 Ped: 1 Per: 12 1 13 0 0 34 0 0 2 0 1 2 1 0 14.50 Ped: 1 Per: 13 1 14 3 4 0 15 15 2 0 1 2 1 0 2.10 Ped: 1 Per: 14 1 15 3 4 40 17 17 1 0 2 2 0 0 0.00 Ped: 1 Per: 15 1 16 0 0 40 0 0 2 0 1 2 1 1 9.80 Ped: 1 Per: 16 1 17 3 4 43 19 19 1 0 2 2 0 0 0.00 Ped: 1 Per: 17 1 18 0 0 43 0 0 2 0 1 2 1 0 11.50 Ped: 1 Per: 18 1 19 3 4 0 0 0 1 0 1 2 1 0 9.20 Ped: 1 Per: 19 1 20 0 0 47 0 0 2 0 0 1 0 0 0.00 Ped: 1 Per: 20 1 21 6 5 47 22 22 1 0 2 2 0 0 0.00 Ped: 1 Per: 21 1 22 6 5 48 24 24 1 0 2 2 0 0 0.00 Ped: 1 Per: 22 1 23 0 0 48 0 0 2 0 1 2 1 0 13.40 Ped: 1 Per: 23 1 24 6 5 0 25 25 2 0 1 2 1 1 10.40 Ped: 1 Per: 24 1 25 6 5 0 0 0 2 0 1 2 1 1 9.90 Ped: 1 Per: 25 1 26 7 8 0 27 27 2 0 1 2 1 1 16.80 Ped: 1 Per: 26 1 27 7 8 53 29 29 2 0 1 2 0 1 30.10 Ped: 1 Per: 27 1 28 0 0 53 0 0 1 0 1 2 1 0 6.90 Ped: 1 Per: 28 1 29 7 8 56 0 0 2 0 1 2 1 1 15.40 Ped: 1 Per: 29 1 30 0 0 56 0 0 1 0 1 2 1 0 14.30 Ped: 1 Per: 30 1 31 9 10 0 32 32 2 0 1 1 1 0 6.80 Ped: 1 Per: 31 1 32 9 10 0 33 33 1 0 1 1 1 0 5.60 Ped: 1 Per: 32 1 33 9 10 0 0 0 2 0 1 1 1 1 31.60 Ped: 1 Per: 33 1 34 12 13 0 35 35 1 0 1 1 1 0 19.40 Ped: 1 Per: 34 1 35 12 13 0 36 36 2 0 1 1 1 1 41.70 Ped: 1 Per: 35 1 36 12 13 0 37 37 1 0 1 1 1 0 20.50 Ped: 1 Per: 36 1 37 12 13 0 38 38 1 0 1 1 1 1 28.40 Ped: 1 Per: 37 1 38 12 13 0 39 39 2 0 1 1 1 0 11.50 Ped: 1 Per: 38 1 39 12 13 0 0 0 2 0 1 1 1 0 21.00 Ped: 1 Per: 39 1 40 15 16 0 41 41 2 0 1 1 1 0 10.50 Ped: 1 Per: 40 1 41 15 16 0 0 0 2 0 1 1 1 0 12.60 Ped: 1 Per: 41 1 42 0 0 52 0 0 1 0 1 1 1 0 11.20 Ped: 1 Per: 42 1 43 17 18 52 44 44 2 0 1 1 1 1 37.20 Ped: 1 Per: 43 1 44 17 18 0 45 45 2 0 1 1 1 0 10.10 Ped: 1 Per: 44 1 45 17 18 0 46 46 1 0 1 1 1 1 34.90 Ped: 1 Per: 45 1 46 17 18 0 0 0 1 0 1 1 1 1 25.30 Ped: 1 Per: 46 1 47 21 20 0 0 0 2 0 1 1 1 1 47.90 Ped: 1 Per: 47 1 48 22 23 0 50 50 2 0 1 1 1 0 14.00 Ped: 1 Per: 48 1 49 0 0 51 0 0 1 0 0 1 0 0 0.00 Ped: 1 Per: 49 1 50 22 23 51 0 0 2 0 1 2 1 1 55.30 Ped: 1 Per: 50 1 51 49 50 0 0 0 2 0 1 1 1 0 13.60 Ped: 1 Per: 51 1 52 42 43 0 0 0 2 0 1 1 1 0 12.50 Ped: 1 Per: 52 1 53 28 27 0 54 54 1 0 1 1 1 1 37.50 Ped: 1 Per: 53 1 54 28 27 0 55 55 1 0 1 1 1 1 14.70 Ped: 1 Per: 54 1 55 28 27 0 0 0 2 0 1 1 1 1 29.90 Ped: 1 Per: 55 1 56 30 29 0 57 57 1 0 1 1 1 0 5.70 Ped: 1 Per: 56 1 57 30 29 0 0 0 2 0 1 1 1 0 8.20 Ped: 1 Per: 57 .TE Here, three loci are represented. The first is an affection status locus (coronary disease symptoms) with three liability classes (ages 0-20, 20-40, and greater than 40); the second is a binary factor locus (LDL receptor polymorphism), and the third is a quantitative variable (age adjusted LDL cholesterol levels). Individuals with unknown affection status are assigned to the first liability class in this example, but the results would be the same irrespective of this assignment. .SH NOTES The information contained herein was gleaned, often-times verbatim, from .UR http://linkage.rockefeller.edu/soft/linkage/ the LINKAGE User's Guide .UE on the web by kind permission of Jurg Ott, Ph.D. .SH AUTHORS Mark Lathrop and Jurg Ott. .PP This manual page was written by Elizabeth Barham for the Debian GNU/Linux distribution. .SH WORLD-WIDE-WEB .UR http://linkage.rockefeller.edu/soft/linkage/ http://linkage.rockefeller.edu/soft/linkage/ .UE .SH SEE ALSO .BR LINKAGE (5), .BR DATAFILE (5), .BR ilink (1), .BR linkmap (1), .BR lodscore (1), .BR mlink (1), and .BR unknown (1).