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. Eqtl will overwrite the file if it exists, and create a new file if it does not. If not used, then Eqtl will use qtlcart.eqt.

-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.

-m

Eqtl 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.

-H

Allows the user to specify which hypothesis test results to process. Use values 10 or 14 for data with two marker classes, and 30, 31, 32, 34 for those with three marker classes.

-S

Tells Eqtl the significance threshold. It assumes that the test statistic is significant if greater than this value. It is 3.84 by default.

-a

Eqtl uses the specified size (alpha) to determine the significance threshold from the experiment-wise permutation results. If used, the -S option is ignored, and the significance threshold is set and saved from the experiment-wise permutation test results. The size is 0.05 by default.

-L

If used with argument 1, it causes LOD scores to be output rather than the LR statistics. It is 0 by default.

-I

This should be followed by a string of no more than eight characters. It allows the user to control which files Eqtl will process. The default is ZM, which means process the results of Zmapqtl and JZmapqtl (the M is for multitrait). You can also add the letters P for permutations, B for bootstraps or J for jackknives. Prior to implementing this option, the default was PBJZM. Note that the order of the letters indicates the order of processing: If you want to use the threshold from a permutation test, then the P should precede the Z and M values. Also, you need to have at least one action.