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  • section 3.1 Constants
    VALUES FOR QUANTITATIVE TRAITS AFFECTION STATUS missaff 0 MISSING VALUE FOR AFFECTION STATUS affval 2 CODE FOR AFFECTED INDIVIDUAL maxliab MAXIMUM NUMBER OF LIABILITY CLASSES BINARY FACTOR UNION SYSTEM maxfact MAXIMUM NUMBER OF BINARY CODES AT A SINGLE LOCUS MAXTRAIT MAXLIAB and MAXFACT can be varied to meet the requirements for various problems The other default values should not be modified unless absolutely necessary Modification of the default values may introduce problems of compatibility when data are transferred between program versions or installation sites MAXNEED and MAXCENSOR are variables that are difficult to determine prior to running the program Probabilities of various recombination classes are stored in an array dimensioned by MAXNEED If you compile the program with a large value of MAXNEED e g 1000 a message giving the optimal value will be printed if all the probabilities are successfully stored within this limit If MAXNEED is too small the program will terminate with an error message MAXCENSOR dimensions an array that increases the efficiency of calculations Small values will not cause a runtime error but may increase computation times The program will give a message to help optimize the choice of this value The constant MININT is used with MAXCENSOR it should be assigned the minimum value supported by the compiler MINFREQ is another constant that can improve the efficiency of calculations when dominant or codominant loci are being analyzed Rare homozygotes will not be considered in the calculations if the gene frequency is less than MINFREQ Heterozygote x heterozygote matings will also be excluded from the calculations in this case For analyzing recessive traits or pedigrees in which heterozygote x heterozygote matings occur you should declare MINFREQ 0 0 scale SCALE FACTOR scalemult SCALE WEIGHT FOR EACH LOCUS The values of SCALE and SCALEMULT can be increased

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec3.1.html (2012-11-26)
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  • section 3.2 ILINK
    1 locations in the list correspond to the recombination rates between adjacent loci In most applications estimates of these recombination rates will be made with other parameters held fixed In this case any of the locus numbers can be used for the iterated locus the value must be between 0 and n where 0 indicates that none of the loci can have iterated parameters For example if 1 is chosen for the iterated locus and n is 3 the two lines to add to the DATAFILE are 1 The last line must end directly after the specification of the last iterated or non iterated parameter without trailing blanks This end of line deliminator tells the program that only recombination fractions will be estimated Sometimes it is useful to fix the value of one of the recombination rates for example if the first two loci are known to be completely linked we might wish to fix the first recombination rate to 0 0 while estimating the second rate In this case the last two lines are 1 With sex specific recombination rates the number of parameters is increased by 1 to n when assuming a constant ratio of female male genetic distances or by n 1 to 2n 2 when estimating different male and female recombination fractions in each interval For the former the last two lines are 1 and for the latter they are 1 With three loci ILINK supports interference When a mapping function is used two iterated parameters are specified for each sex Without a mapping function three recombination rates can be estimated for each sex and the number of iterated parameters should be adjusted accordingly Specifications for Estimating Other Parameters All locus types support the estimation of gene frequencies these add an additional nallele 1 parameters to

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec3.2.html (2012-11-26)
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  • section 3.3 MLINK
    calculates lod scores otherwise only the likelihood values are given MLINK is distributed with SCORE set to true Datafile Structure The program specific part of DATAFILE consists of a single line that contains the number of the recombination fraction to be varied an increment for the recombination fraction and a stopping value The likelihood is evaluated for the initial recombination values then the designated value is incremented and the likelihood recalculated if the incremented value is less than the final value The incremental calculations are continued until the designated recombination is greater than the final value As an example suppose that lod scores are calculated for two loci If the following is the last line in DATAFILE 1 0 1 0 5 the program will start with the initial recombination value specified in DATAFILE and calculate with increments of 0 1 until 0 5 is surpassed To calculate for increments of 0 01 stopping at 0 2 this line should be 1 0 01 0 2 For three loci with the first two loci in the chromosome order completely linked a lod score for linkage with the third locus could be calculated with MLINK at increments of 0 05 with the following line in DATAFILE 1 0 05 0 5 Often different increments are desired in different regions of the lod score table This refinement can be achieved in MLINK by adding additional lines at the end of DATAFILE Each line specifies a new starting recombination fraction increment and final value the recombination to be varied is the same as previously designated Thus the following two lines 1 0 05 0 2 0 2 0 1 0 5 calculates the likelihood with steps of 0 05 until reaching 0 2 followed by steps of 0 1 until reaching 0 5

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec3.3.html (2012-11-26)
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  • section 3.4 LINKMAP
    by moving the locus varied within the interval between flanking markers or to one or the other of the ending intervals in the map The interval between the starting and ending recombination values is divided into equal portions so that the total number of evaluations is equal to gridsize The program must be restarted with a different chromosome order to test other intervals For the outside interval on the left hand side of the map the recombination will decrease automatically from the initial value to the final value therefore the final value should be smaller than the initial value For other intervals the recombination rate will increase from the starting value to the final value In interior intervals the recombination between the flanking markers is held constant assuming Haldane s mapping function If the final recombination rate specified in DATAFILE is greater than the total recombination in the interval the latter figure determines the division As an example consider a map of four fixed loci with a fifth locus whose position is varied The DATAFILE could have the form 5 0 0 0 0 0 0 0 0 5 3 2 4 1 The program will make 10 likelihood evaluations

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec3.4.html (2012-11-26)
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  • section 3.5 cilink
    DATAFILE The output files are FINAL OUTFILE STREAM TEMPPED and TEMPDAT are temporary files produced by CFACTOR for input to CILINK Program Constants Specific to CILINK CILINK contains many of the program constants that ILINK does for controlling numerical maximization Datafile Structure The program code for CILINK is 1 Otherwise the DATAFILE format is the same as that for the ILINK program except that all loci must be codominant Either

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec3.5.html (2012-11-26)
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  • section 3.6 cmap
    calling order is CFACTOR CMAP The input files for this suite of programs are PEDFILE DATAFILE The output files are OUTFILE STREAM TEMPPED and TEMPDAT are temporary files produced by CFACTOR for input to CMAP Program Constants Specific to CMAP See LINKMAP section 3 4 Datafile Structure Except for the program code which is 2 for CMAP DATAFILE has the LINKMAP format Program Options When the constant BYFAMILY is true

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec3.6.html (2012-11-26)
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  • section 3.7 Lodscore
    the maximum lodscore from two locus data In the present implementation it is almost identical to ILINK Datafile structure In contrast to ILINK for which the program specific parts of the DATAFILE consist of two lines cf p 30 LODSCORE has four lines The first two program specific lines are the same as for ILINK whereas the last two list the two sets of loci set 1 on line 3

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec3.7.html (2012-11-26)
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  • section 3.8 clodscore
    5 2 3 8 CLODSCORE CLODSCORE is analogous to LODSCORE except that it is restricted to three generation pedigrees and codominant marker loci previous 3 7 lodscore next 4 data

    Original URL path: http://linkage.rockefeller.edu/soft/linkage/sec3.8.html (2012-11-26)
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