NAME

Qstats - Calculate basic statistics for a QTL dataset.

SYNOPSIS

Qstats [ -o output ] [ -i input ] [ -m mapfile ]

DESCRIPTION

Qstats does some basic statistics on a dataset of quantitative traits. It plots a histogram and calculates the sample size, mean, variance standard deviation, skewness, kurtosis, and average deviation for a quantitative trait. The program also summarizes missing marker and trait data, as will as determining the marker types (dominant or codominant). Finally, Qstats will test whether markers are segregating at random. It requires a molecular map that could be a random one produced by Rmap, or a real one in the same format as the output of Rmap. The sample could be a randomly generated one from Rcross or a real one in the same format as the output of Rcross.

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 for output. Qstats will append the file if it exists, and create a new file if it does not. If not used, then Qstats will use qtlcart.qst.

-i

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

-m

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

INPUT FORMAT

The input format of the molecular map should be the same as that of the output format from the program Rmap. The input format of the individual data should be the same as the output format of the program Rcross.

EXAMPLES

        % Qstats -i corn.cro -m corn.map

Calculates basic statistics on the dataset in corn.cro using the genetic linkage map in corn.map. The program will display and interactive menu for setting options and print out messages to the screen while running. These can be turned off with -A and -V, respectively. If the dataset in corn.cro has more than one trait, then all traits will be analyzed.

REFERENCES

M. Lynch and B. Walsh (1998) Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.

BUGS

Are there any other statistics that we can do? Your suggestions are welcome.

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.