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 stem for output. Preplot will overwrite the file if it exists, and create a new file if it does not. If not used, then Preplot will use qtlcart. The GNUPLOT file will be qtlcart.plt in that case.

-m

Zmapqtl 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.

-l

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

-q

This requires an input filename. This file may or may not exist. It should be in the same format as the output of Rqtl. The default file is qtlcart.qtl.

-z

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

-T

Allows the user to set the output terminal. Valid options can be found in the GNUPLOT manual. The default is x11 on UNIX, mac for Macintosh and windows for MS-Windows.

-S

When given an argument, Preplot will use this significance threshold. It is 3.84 by default.

-H

Preplot will get results for this hypothesis test from the Zmapqtl outputfile. Test 1 is the default, which is the only value for a backcross.

-L

If given an argument of 1, Preplot will output LOD scores instead of the LR test statistics.