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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.
- 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.
- 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.
- 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.
- 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.
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.
- 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.
- Set the trait to process if using -b 7.
Next: INPUT FORMAT