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
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.
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.
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
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
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