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. LRmapqtl will append the file if it exists, and create a new file if it does not. If not used, then LRmapqtl will use qtlcart.lr.

-i

This requires an input filename. This file must exist. It should be in the same format as the output of Rcross. The default file is qtlcart.cro.

-m

LRmapqtl requires a genetic linkage map. This option requires the name of a file containing the map. It should be in the same format that Rmap outputs. The default file is qtlcart.map.

-r

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.

-t

Use this to specify which trait LRmapqtl will analyze. If this number is greater than the number of traits, then all traits will be analyzed. The default is to analyze trait 1 only.