Rqtl - Place a set of estimated or randomly generated QTLs on a molecular map.
Rqtl [ -o output ] [ -i input ] [ -m mapfile ] [ -b beta ] [ -t Traits ] [ -q QTLperTrait ] [ -d dominance ] [ -1 beta1 ] [ -2 beta2 ] [ -E prop ]
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.
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.
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.
% 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.
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.
Rmap(1), Rcross(1), Qstats(1), LRmapqtl(1), SRmapqtl(1), Zmapqtl(1), JZmapqtl(1), Eqtl(1), Prune(1), Preplot(1), QTLcart(1)
In general, it is best to contact us via email (basten@statgen.ncsu.edu)
Christopher J. Basten, B. S. Weir and Z.-B. Zeng
Department of Statistics, North Carolina State University
Raleigh, NC 27695-8203, USA
Phone: (919)515-1934