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. Prune will overwrite the file ending in .crb if it exists, and create a new file if it does not. If not used, then Prune will use qtlcart.crb. If the map is recreated, then a new map file will be written to qtlcart.mpb by default or a file ending in mpb with the specified stem.

-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

Prune 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.

-I

Sets the interactive level. A zero means that Prune will do what it needs to without asking (the default for bootstraps, permutations or missing data simulations). A one means that the user will be put into a repeating loop to manipulate the data set. It has a value 1 by default, but using the -b option disables it.

-M

This sets a level for the elimination of individuals with this much missing marker data, or for the simulation of missing or dominant markers when used with the -b option.

-b

Prune will read in the map and data file and do one of AUTOMATIC ACTIONS described in the section of the same name below. A value of zero means that this option is ignored.

-t

Set the trait to process if using -b 7.