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.
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.
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.
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.
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
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.
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.
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
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