LRmapqtl

NAME

LRmapqtl - Single marker QTL analysis.


SYNOPSIS

LRmapqtl [ -o output ] [ -i input ] [ -m mapfile ] [ -r reps ] [ -t trait ]


DESCRIPTION

LRmapqtl uses simple linear 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.


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

-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
LRmapqtl 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.

-r
LRmapqtl will do a permutation test a la Churchill and Doerge (1994). This option specifies the number of permutions to do. It is zero by default, which means no permuation test is done. If used, you must specify a positive integer. Usually, 1,000 is sufficient.

-t
Use this to specify which trait LRmapqtl 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.


MODEL

The basic linear model is

        Trait = Mean + Slope x Marker + Error

The marker value will be in the range [-1, 1] inclusive. Two hypotheses are compared. The null hypothesis is that the Slope is zero. The alternate is that the Slope is non-zero. A p-value for the likelihood ratio of these to hypotheses is calculated for each marker-trait combination. LRmapqtl outputs a table with parameter estimates, F statistics, Likelihood ratios and p-values.


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

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

Calculates the regression coefficients for each marker on the dataset in corn.cro using the genetic linkage map in corn.map.


REFERENCES

  1. Churchill, G. A. and R. W. Doerge (1994) Empirical threshold values for quantitative trait mapping. Genetics 138, 963-971.


BUGS


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.



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