NAME

Preplot - Process results of LRmapqtl and Zmapqtl for input to gnuplot

SYNOPSIS

Preplot [ -o output ] [ -m mapfile ] [ -l lrfile ] [ -z zfile ] [ -q qtlfile ] [ -S threshold ] [ -T terminal ] [ -H hypo ] [ -L lod ]

DESCRIPTION

Preplot reformats the output of LRmapqtl and Zmapqtl so that it can be plotted by GNUPLOT. It requires a molecular map that was used in the analysis of the data with LRmapqtl and Zmapqtl.

OPTIONS

See QTLcart(1) for more information on the global options -h for help, -A for automatic, -V for non-Verbose -W path for a working directory, -R file to specify a resource file, -e to specify the log file, -s to specify a seed for the random number generator and -X stem to specify a filename stem. The options below are specific to this program.

If you use this program without specifying any options, then you will get into a menu that allows you to set them interactively.

-o

This requires a filename stem for output. Preplot will overwrite the file if it exists, and create a new file if it does not. If not used, then Preplot will use qtlcart. The GNUPLOT file will be qtlcart.plt in that case.

-m

Zmapqtl requires a genetic linkage map. This option requires the name of a file containing the map. It should be in the same format that Rmap outputs. The default file is qtlcart.map.

-l

This requires an input filename. This file must exist. It should be in the same format as the output of LRmapqtl. The default file is qtlcart.lr.

-q

This requires an input filename. This file may or may not exist. It should be in the same format as the output of Rqtl. The default file is qtlcart.qtl.

-z

This requires an input filename. This file must exist. It should be in the same format as the output of Zmapqtl. The default file is qtlcart.z.

-T

Allows the user to set the output terminal. Valid options can be found in the GNUPLOT manual. The default is x11 on UNIX, mac for Macintosh and windows for MS-Windows.

-S

When given an argument, Preplot will use this significance threshold. It is 3.84 by default.

-H

Preplot will get results for this hypothesis test from the Zmapqtl outputfile. Test 1 is the default, which is the only value for a backcross.

-L

If given an argument of 1, Preplot will output LOD scores instead of the LR test statistics.

EXAMPLES

        % Preplot -L 1

Preplot will automagically reformat your results to be plotted by GNUPLOT, converting the likelihood ratio test statistics into LOD scores along the way.

REFERENCES

T. Williams and C. Kelley (1993) GNUPLOT: An Interactive Plotting Program. Version 3.5

CAVEATS

Preplot will search for the ouput files from Rqtl, Eqtl and MImapqtl and try to process them. If you don't want them processed, rename or move the files. Note that Preplot only searches for files with names stem.eqt, stem.qtl and stem.mqt, where stem is the filename stem.

BUGS

Preplot ignores JZmapqtl output.

SEE ALSO

Emap(1), Rmap(1), Rqtl(1), Rcross(1), Qstats(1), LRmapqtl(1), BTmapqtl(1), SRmapqtl(1), JZmapqtl(1), Eqtl(1), Prune(1), Preplot(1), MImapqtl(1), MultiRegress(1), Examples(1) SSupdate.pl(1), Prepraw.pl(1), EWThreshold.pl(1), GetMaxLR.pl(1), Permute.pl(1), Vert.pl(1), CWTupdate.pl(1), Ztrim.pl(1), SRcompare.pl(1), Ttransform.pl(1), TestExamples.pl(1), Model8.pl(1), Dobasics.pl(1), Bootstrap.pl(1)

CONTACT INFO

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

        Christopher J. Basten, B. S. Weir and Z.-B. Zeng
        Bioinformatics Research Center, North Carolina State University
        1523 Partners II Building/840 Main Campus Drive
        Raleigh, NC 27695-7566     USA
        Phone: (919)515-1934

Please report all bugs via email to qtlcart-bug@statgen.ncsu.edu.

The QTL Cartographer web site ( http://statgen.ncsu.edu/qtlcart ) has links to the manual, man pages, ftp server and supplemental materials.