CD ROM Paradise Collection 4/CD ROM Paradise Collection 4 1995 Nov.iso/science/fastmap.zip/TABLE.DOC

Text File | 1992-07-15 | 7KB | 126 lines

                                    TABLE.DOC

                           Documentation for TABLE.EXE

        This is a very simple program which takes the output from MLINK
        or LINKMAP and tabulates it in a more easily digestible form. It
        can also produce files suitable for graphing lod scores or for
        input to HOMOG, BTEST and FASTMAP.

        The input file is the OUTPUT.DAT file which the LINKAGE programs
        produce. When using LINKSYS this file is renamed to be
        FILENAME.RES. With LCP or the LINKSYS program MCP it is possible
        to run a whole load of analyses all at once and output them into
        one results file. If you do this TABLE will not work correctly -
        it expects to find the output from only one analysis by either
        LINKMAP or MLINK. If you have set up a batch file to run several
        analyses at once, you must edit the output so that the results
        from each analysis is in a different .RES file. TABLE has
        actually only been tested with the results files produced by
        LINKSYS v. 4.11 and LINKAGE v. 4.7 and 5. With LINKMAP it
        assumes that the test locus is named first and that the whole
        map has been produced. With MLINK it assumes that the "lod score
        table" output option has been selected. TABLE may work in other
        circumstances - I just haven't tried it.

        If you are working with more than one pedigree at a time then
        make sure that the "byfamily" switch in the Linkage programs is
        set to true so that likelihood scores are output for each family
        - it will not increase the time that it takes the program to
        run. Otherwise only the total lod scores across pedigrees will
        be available.

        If your results have ended up in FILENAME.RES then to use TABLE
        just enter:

        TABLE FILENAME

        A new file will be created on your disk called FILENAME.TAB.
        This contains a table of lod scores at different recombination
        frequencies, or with LINKMAP at different distances taking
        distance 0 to be at 0% recombination with the leftmost fixed
        marker. The lod scores are calculated by subtracting the log10
        likelihood at theta=50% from the log10 likelihood at other
        recombination fractions. Reombination fractions are converted to
        distances in centimorgans using the Kosambi mapping function.

        There are five optional switches which can be used with TABLE
        to produce other files:

        TABLE FILENAME /G /H /A /B /I

        If /G is selected a file called FILENAME.GRP will be created.
        This provides the input for a Shareware graphing program
        available from me called EASIGRAF, which forms part of the
        EASISTAT package. To see the graph of lod scores one simply
        enters:

        EASIGRAF FILENAME.GRP

        If /H is selected a file called FILENAME.HOM is produced which
        can be read in by Jurg Ott's HOMOG program to perform the A-test
        of homogeneity of linkage. (See Ott, 1985 Analysis of Human
        Genetic Linkage, John Hopkins University Press and Ott, Ann Hum
        Genet 47:311-320, 1983). A version of the program is available
        from Jurg Ott but unfortunately this no longer uses the same
        format as the listing in the book so some editing would be
        necessary. The source code for a version transcribed into C
        which uses the original format is included together with the
        executable.

        If /A is selected then the TABLE program itself performs the A-
        test calculations. It outputs the adjusted lod score (log 10 of
        the likelihood ratio) obtained under the assumption of
        heterogeneity, called A-lod, together with alpha, the fraction
        of linked families which produce this maximum lod. It does not
        explicitly perform the test for statistical significance which
        the HOMOG program does. To do this by hand, subtract the maximum
        conventional (total) lod from the maximum value of A-lod and
        multiply by 2ln(10) (twice the natural log of 10, about 4.605).
        This may be taken as a chi-squared statistic with one degree of
        freedom providing evidence to support the hypothesis of
        heterogeneity if linkage is assumed.

        If /I is selected a file called FILENAME.INP is created which
        contains recombination fraction and lod score pairs as needed
        for input into the FASTMAP program. This produces estimates of
        multipoint lod scores from two-point scores, and has been
        submitted for publication to Human Heredity. It is available
        from me or (preferably) from the gene-server ftp site or one of
        its mirrors ([e-mail] or
        gene-server%bchs.uh.edu@CUNYVM, send mail with subject: SEND DOS
        HELP). Normally, only recombination fractions between 0.01 and
        0.4 are output. It probably isn't advisable to change this, but
        if you do want to try it you can change the values for
        MIN_RF_TO_FIT and MAX_RF_TO_FIT in TABLE.C and recompile it.

        If /B is selected a file called FILENAME.BTE is produced which
        can be input into Neil Risch's BTEST program for homogeneity of
        linkage. (See Risch, Am J Hum Genet, 42:353-364, 1988). Copies
        of this program are available from Neil Risch at Yale University
        School of Medicine, Department of Epidemiology and Public
        Health, 60 College Street, PO Box 3333, New Haven, CT 06510;
        [phone]; BITNET: RISCH@YALEMED.

        Note that to produce input for HOMOG and BTEST the .RES file
        must (obviously) contain output from more than one pedigree and
        the likelihoods by family must be available. For BTEST the
        output must be from MLINK, and not LINKMAP.

        I hope people find this useful.


        Dave Curtis July 1992


        Academic Department of Psychiatry
        St Mary's Hospital Medical School
        Praed Street
        London W2 1NY, England                   Phone:  [phone]

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