NAME - Iterate Zmapqtl model 8 to determine a stable set of cofactors

SYNOPSIS  [-b bindir] [-X stem] [-S sig. threshold] [-i iterations] 
    [-m max nbp] [-H hypothesis] [-h]

DESCRIPTION iterates using Zmapqtl and Eqtl to determine a stable set of cofactors for composite interval mapping. First, interval mapping is run and the nearest markers to significant peaks are identified. These markers are used as cofactors in the first iteration of composite interval mapping. A new set of cofactors are identified by proximity to the likelihood peaks and the process is repeated.


This option requires the path to the QTL Cartographer binaries and perl scripts.

requires an integer to control how many iterations you want to do.

This option allows you to specify the filename stem.

This option requires a real number to indicate the significance threshold for the likelihood ratio.

This option allows you to specify the maximum number of background parameters in composite interval mapping.

Use this option to specify which hypothesis test you want to use. The usual values are 10 or 30.

requires no operand. If used, it prints a usage message and exits.


Suppose the files and mletest.cro are in the current working directory.

    %  -b /home/basten/bin  -X mletest -S 13.0 -m 25 -H 10 -i 15

Will assume that the QTL Cartographer programs are in /home/basten/bin. It will use a significance threshold of 13.0 and allow for up to 25 markers in composite interval mapping. It will iterate 15 times in an attempt to find a stable set of cofactors. This script uses another script called which compares the set of cofactors (in SRmapqtl.out format) between consecutive runs and reports how many cofactors have been added or deleted.


Zmapqtl(1), Qstats(1), Eqtl(1),


In general, it is best to contact us via email (

        Christopher J. Basten, B. S. Weir and Z.-B. Zeng
        Department of Statistics, North Carolina State University
        Raleigh, NC 27695-7566, USA
        Phone: (919)515-1934

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