LRmapqtl - Single marker QTL analysis.
LRmapqtl [ -o output ] [ -i input ] [ -m mapfile ] [ -r reps ] [ -t trait ]
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.
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 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.
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.
% 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.
Rmap(1), Rqtl(1), Rcross(1), Qstats(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