NAME

SRmapqtl - Map quantitative traits on a molecular map.

SYNOPSIS

SRmapqtl [ -o output ] [ -i input ] [ -m mapfile ] [ -t trait ] [ -M Model ] [ -F pFin ] [ -B pFout ] [ -u MaxSteps ]

DESCRIPTION

SRmapqtl uses stepwise regression to map quantitative trait loci to a map of molecular markers. 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.

This program should be run before .Zmapqtl if you want to use composite interval mapping. The results will be used to pick markers background control in composite interval mapping. The main result from using this program is to rank the markers in terms of their influence on the trait of interest.

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. SRmapqtl will append the file if it exists, and create a new file if it does not. If not used, then SRmapqtl will use qtlcart.sr.

-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

SRmapqtl 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.

-t

Use this to specify which trait SRmapqtl will analyze. If this number is greater than the number of traits, then all traits will be analyzed. The default is to analyze trait 1 only.

-M

This tells SRmapqtl what type of analysis to perform. Use a 0 for forward stepwise (FS) regression, a 1 for backward elimination (BE) and a 2 for forward regression with a backward elimination step at the end (FB). It is probably best to use Model 2 here.

-F

Requires a real number in the range 0.0 to 1.0. This is a threshold p value for adding markers in model 2 during the forward stepwise regression step. The default is 0.05.

-B

Requires a real number in the range 0.0 to 1.0. This is a threshold p value for deleting markers in model 2 during the backward elimination step. It should probably be the same as the previous option. The default is 0.05.

-u

Requires an integer valued argument. This allows you to specify a hard limit to the number of steps in a forward regression analysis. It is valid for models 0 and 2. By default, it is 100.

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

        % SRmapqtl -i corn.cro -m corn.map -M 2

Does a forward stepwise regression with a backward elimination step for the dataset in corn.cro using the genetic linkage map in corn.map.

REFERENCES

BUGS

Forward and backward regression should probably use the thresholds for adding and deleting markers from the model. When that feature is added, the -F and -B options will have more use.

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.