Bootstrap

NAME

Bootstrap.pl - Do a bootstrap analysis with Zmapqtl


SYNOPSIS

  Bootstrap.pl [-b bin] [ -X stem] [-m model] [-r iterations] [-e email] 
       [-H hypothesis] [-a rep] [-s] [-h]


DESCRIPTION

Bootstrap.pl iterates using Prune and Zmapqtl to determine sampling variances based on a bootstrap resampling.


OPTIONS

If the qtlcart.rc file if it exists, Bootstrap.pl will first set its parameter values from that file. Any command line options will override the qtlcart.rc values. If a parameter has not been set by either the qtlcart.rc file or command line parameters, default values are set.

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

-r
requires an integer to control how many bootstrap iterations you want to do. The default is 1000.

-X
This option allows you to specify the filename stem. The default is qtlcart.

-e
This option requires an email address. The temporary log file will be sent to this address to indicate that the bootstrap is complete. If blank, then no email message will be sent. The default is not to use this option.

-m
This option allows you to specify the Zmapqtl model to use. The default is interval mapping (3).

-H
Use this option to specify which hypothesis test you want to use. The usual values are 1 or 30. The default is 1: Unless there are three genotypic classes, do not change this option..

-s
requires no operand. This tells Bootstrap.pl to save the bootstrapped datasets and their analytical results. If used with a large number of bootstraps, a great deal of harddisk space will be used up. It is mainly for debugging purposes.

-a
requires an integer operand indicating the last completed iteration. Useful if your machine crashed during the bootstrap.

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


EXAMPLE

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

    % Zmapqtl -X mletest -M 3 -A -V 
    % Bootstrap.pl  -b /home/basten/bin  -r 500

These commands assume that the QTL Cartographer programs are in /home/basten/bin. It will use interval mapping and do 500 bootstrap iterations. Note that you need to do an initial Zmapqtl run before beginning the bootstrap, and that initial run will set the filename stem and the model for analysis.

If your machine crashed during the bootstrap analysis, then you can restart where you left off (provided that the crash occurred during the Zmapqtl run). Suppose the above completed 356 iterations and crashed during iteration 357. Then

    % Bootstrap.pl  -b /home/basten/bin  -r 500 -a 356

would pick up the bootstrap at iteration 357 and complete at 500.


CAVEATS

The -s option allows you to save the bootstrapped datasets and analytical results. For iteration i, model m, filename stem qtlcart and single trait analysis, there will be files qtlcart.cro.i, qtlcart.zm.i and qtlcart.zm.bi.

This option is mainly for debugging purposes. Be aware that a large number of iterations will use a great deal of disk space. You could modify the Bootstrap.pl script to compress these files to save disk space.


SEE ALSO

Zmapqtl(1), Prune(1), SSupdate.pl(1)


AUTHORS

In general, it is best to contact us via email (basten@statgen.ncsu.edu)

        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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