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

-i

This requires an input filename. This file must exist. The format is defined below. The default file is qtlcart.zr.

-t

Use this to specify which trait MultiRegress will analyze. If this number is greater than the number of traits, then all traits whose names do not begin with a minus sign will be analyzed. If 0, then no traits except those beginning with a plus sign will be analyzed. The default is to analyze trait 1 only.

-c

This tells MultiRegress whether to use the categorical traits in the analysis. Use a 1 to include categorical traits and a 0 to exclude them.

-S

Requires a real number in the range 0.0 to 1.0. This is a threshold p value for adding or deleting sites from the model. The default is 0.05.

-w

Requires a non-negative real number. This defines a window around a site already in a regression model to block from further analysis.

-u

Requires an integer valued argument. This allows you to specify a hard limit to the number parameters in the regression analysis. By default, it is 100.

-I

Requires a value of 10 or 30. The value 10 means just analyze additive effects, while the value 30 means analyze for dominance and additive effects.