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  • 4.Preprocessing Programs
    linkage user s guide version 5 2 Chapter 4 Data Preprocessing Programs Table of Contents 4 0 Overview 4 1 UNKNOWN 4 2 CFACTOR previous 3 analysis programs up top

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/c4.html (2012-11-26)
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  • section 4.0 Overview
    Overview Several preprocessing programs are required prior to invoking an analysis program The calling order for the data preprocessing and analysis programs are explained in Chapter 3 A brief description of each of the preprocessing programs follows previous 3 analysis

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec4.0.html (2012-11-26)
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  • section 4.1 unknown
    UNION SYSTEM maxfact MAXIMUM NUMBER OF BINARY CODES AT A SINGLE LOCUS QUANTITATIVE TRAIT maxtrait MAXIMUM NUMBER OF QUANTIT FACTORS AT A SINGLE LOCUS missval 0 0 MISSING VALUES FOR QUANTITATIVE TRAITS affall 2 ALLELE GIVING AFFVAL FOR QUANT TRAITS IN MALES SEXLINK AFFECTION STATUS missaff 0 MISSING VALUE FOR AFFECTION STATUS affval 2 CODE FOR AFFECTED INDIVIDUAL maxliab MAXIMUM NUMBER OF LIABILITY CLASSES OTHERS maxn MAXIMUM NUMBER OF ITERATED

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec4.1.html (2012-11-26)
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  • section 4.2 cfactor
    when a parent cannot be inferred elimb false Eliminate locus when neither parent can be inferred esame false Eliminate locus when parents could be homozygote OTHERS maxn MAXIMUM NUMBER OF ITERATED PARAMETERS MAXPED cannot be determined before CFACTOR is applied to the data but twice the actual number of pedigrees is probably a safe minimum value CFACTOR takes IPEDFILE and DATAFILE as input and produces TEMPPED and TEMPDAT When CFACTOR

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec4.2.html (2012-11-26)
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  • wlihomepage
    25 02 Bib Variance components analysis jul 25 02 Bib Linkage algorithms may 23 02 Perl as a tool for linkage analysis nov 27 01 web preplink you are the visitor no since sept 27 1996 last modified local time now CeNtEr fOr GeNoMiCs aNd HuMaN GeNeTiCs NoRtH ShOrE UnIvErSiTy HoSpItAl ReSeArCh BuiLdInG 350 CoMmUnItY DrIvE MaNhAsSeT NY 11030 http www nslij genetics org wli wli at nslij genetics org

    Original URL path: http://linkage.rockefeller.edu/wli/ (2012-11-26)
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  • fastlink readme: aallele
    alleles A1 through An that occur in the population at large Suppose that in a population to be studied with linkage analysis only alleles A1 through Ak with k A concrete FASTLINK example Suppose the general population has the possibilities Allele 1 2 3 4 5 6 Frequency 3 2 15 1 22 03 and this is encoded in the locus file datain dat Suppose that the pedigree s encoded in the pedigree file pedin dat contain only the alleles 2 4 and 5 LINKAGE and FASTLINK require that the alleles be numbered consecutively starting at 1 Therefore in the process of reducing from 6 to 4 alleles it is necessary to renumber the alleles Renumber old allele 2 to be new allele 1 with frequency 2 Renumber old allele 4 to be new allele 2 with frequency 1 Renumber old allele 5 to be new allele 3 with frequency 22 Create catch all allele 4 with frequency 48 sum of frequencies of old 1 old 3 old 6 No person should have the catch all allele but it is absolutely wrong to omit the catch all allele Important technical note the process of renumbering alleles to reduce their number loses no information in a statistical sense unless one is estimating allele frequencies Renumbering is distinct from downcoding in which multiple alleles that are distinct and do occur in the population are given the same number in the interest of reducing running time In general downcoding loses information although there are some special situations in which it does not because the frequencies of some different alleles happen to be identical Extra alleles and separating pedigrees The use of extra alleles often arises when the original data had P pedigrees amongst which all n alleles occur but the population in some

    Original URL path: http://linkage.rockefeller.edu/soft/fastlink/fl_allele.html (2012-11-26)
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  • fastlink readme: bug report
    I ve gotten so far have helped tremendously However I would like to speed up the process by guiding you in what I need to know to track down a bug successfully In general there are four categories of bugs Compilation Problems Crash during a run Results obviously bogus or inconsistent with LINKAGE Anything else Here is what you should send me for each type of bug report Compilation Problems A script showing your compilation attempt and the errors you got Some indication which version number of FASTLINK you are using Your Makefile If the compilation complains that something is not defined send me your current versions of the files commondefs h moddefs h and slowmoddefs h Crash or Results obviously bogus or inconsistent with LINKAGE Which program and version number fast or slow you are using Your data files e g pedin dat datain dat Whatever shell script you are using to run the programs An indication of whether the results you are getting are bogus or are plausible but inconsistent with LINKAGE Anything else Which program and version number fast or slow you are using Your data files e g pedin dat datain dat An explanation with sample

    Original URL path: http://linkage.rockefeller.edu/soft/fastlink/fl_bugreport.html (2012-11-26)
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  • fastlink readme: checkpoint
    important to ensure that none of these files are present at the start of a fresh run however do not delete any of these after a run has begun and especially when trying to recover from a previous run NOTE Please note that the file protections set by the program may not be what you desire These can be changed by altering the value of the variable CopyAppendPerms in the file checkpointdefs h where the value specified should be as given to the chmod 1 command The additional leading 0 is essential it makes the value that follows to be treated as a constant in octal as required by chmod 1 checkpoint For ILINK and LODSCORE This file is written at two types of places namely an iteration and a function checkpoint Only three parts of this file are in text mode they are The date time stamp on the first line The two type information fields on the second line and The string END OF DATA on the last line of the file Following these are the bytes that constitute the actual values being stored these are in an architecture dependent binary format Finally the end marker provides us with a means of partially checking for the integrity of the data written in the checkpoint For LINKMAP and MLINK only some counters indicating how many function evaluations are complete need to be stored in this file checkpoint When a checkpoint is to be written and a checkpoint file is already found the existing file is moved to this backup name and the new one is written in its place The main purpose of doing this is to increase security against crashes should the crash have damaged the checkpoint file but have left the backup untarnished the backup may be copied into the checkpoint and computation can be resumed even if from a slightly earlier stage in the run The format of this file is the same as that of the checkpoint file which is copied into the backup without modification outf LODSCORE stream dat text outf ILINK stream dat text main LINKMAP stream dat text main MLINK stream dat text outf ILINK final dat text main LINKMAP final dat text main MLINK final dat text outf LODSCORE recfile dat text These files are created by the subroutine outf or main Their purpose is to maintain copies of the files stream dat and final dat for ILINK LINKMAP or MLINK or recfile dat for LODSCORE respectively so that if recovery needs to take place after these files have been written to the two files can be restored to the state they had script stream out text Since the standard scripts being used delete the files final out and stream out at the start of execution the program makes a copy of the current state of these files into the names listed Thus when recovering in the midst of a script the files can be restored to their state when the

    Original URL path: http://linkage.rockefeller.edu/soft/fastlink/fl_checkpoint.html (2012-11-26)
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