NAME

Rqtl - Place a set of estimated or randomly generated QTLs on a molecular map.

SYNOPSIS

Rqtl [ -o output ] [ -i input ] [ -m mapfile ] [ -b beta ] [ -t Traits ] [ -q QTLperTrait ] [ -d dominance ] [ -1 beta1 ] [ -2 beta2 ] [ -E prop ] [ -M Rmode ]

DESCRIPTION

Rqtl will translate a genetic model or simulate a random model for use by Rcross to simulate a data set. It places a specified number of QTLs (Quantitative Trait Loci) on the molecular map created or translated by Rmap. For simulations, they are placed randomly on the map, and the additive, dominace and epistatic effects are also determined. The molecular map could be a random one produced by Rmap, or a real one in the same format as the output of Rmap.

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. Rqtl will overwrite the file if it exists, and create a new file if it does not. If not used, then Rqtl will use qtlcart.qtl.

-i

This requires an input filename. This file must exist. Rqtl will attempt to identify the format of the file and translate it to another format. This file should contain a genetic model defining a set of QTL and including their positions and effects. See the file qtls.inp for the format.

-m

This requires a filename that must exist. Rqtl will read the genetic linkage map from this file.

-t

This allows the user to specify the number of traits to simulate. It is 1 by default.

-q

This requires an integer argument. It allows the user to specify the number of QTL that affect the trait. If one trait is simulated, then exactly this number of QTL will be created. If more than one trait are simulated, then the number of QTL per trait will vary but have mean value specified here. The default is 9.

-d

You can specify the type of dominance at the trait loci. If we assume inbred parental lines with line one marker trait alleles all Q and line two trait alleles all q, then use a 1 for no dominance, a 2 for complete dominance of Q over q, a 3 for complete dominance of q over Q, and a 4 for dominance that is random in direction and magnitude for each locus. It is 1 by default, that is no dominance.

-b

Specifies the parameter needed to determine the additive effect of a QTL. It is 0.5 by default. See Zeng (1992) equation (12) and accompanying text for a discussion of this parameter. Itis not the allelic effect of a QTL allele, rather it is the shape parameter in the beta distribution.

-1, -2

Allows you to specify the two parameters used to determine the dominance effect of a QTL. The effect is simulated from a beta distribution. See the manual for more details.

-E

For a k QTL model, there will be 2k(k+1) potential epistatic terms. This option sets the proportion of epistatic interactions that will be non-zero in a simulated model. The effects are generated with the same beta funtion used for the dominance effects.

-M

By default, Rqtl will not place a new QTL on the same interval or an adjacent interval. If you use this option with a value of 1, then it will allow QTL in adjacent intervals. The value of this option will be returned to 0 at the completion of the program.

INPUT FORMAT

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

If a file is specified with the -i option, then that file will be read for the positions and effects of the QTLs. The format of this file should be identical to that of the output of Rqtl, or of a special format defined in the file qtls.inp included with the distribution.

EXAMPLES

        % Rqtl   -d 2

Places 9 QTLs on the map in Rmap.out. There is complete dominance of A over a.

        % Rqtl   -i qtls.inp -o test.qtl

Reads the file qtls.inp and translates it into the output format of Rqtl. The output is written to the file test.qtl, which is overwritten if it exists.

REFERENCES

Zeng, Zhao-Bang (1992) Correcting the bias of Wright's estimates of the number of genes affecting a quantitative trait: A further improved method. Genetics 132, 823-839.

BUGS

The -t option for the number of traits is rather primitive at this time. The number of QTLs and their effects are randomly determined, with means given in the other options.

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.