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

-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

SRmapqtl 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.

-t

Use this to specify which trait SRmapqtl will analyze. If this number is greater than the number of traits, then all traits will be analyzed. The default is to analyze trait 1 only.

-M

This tells SRmapqtl what type of analysis to perform. Use a 0 for forward stepwise (FS) regression, a 1 for backward elimination (BE) and a 2 for forward regression with a backward elimination step at the end (FB). It is probably best to use Model 2 here.

-F

Requires a real number in the range 0.0 to 1.0. This is a threshold p value for adding markers in model 2 during the forward stepwise regression step. The default is 0.05.

-B

Requires a real number in the range 0.0 to 1.0. This is a threshold p value for deleting markers in model 2 during the backward elimination step. It should probably be the same as the previous option. The default is 0.05.

-u

Requires an integer valued argument. This allows you to specify a hard limit to the number of steps in a forward regression analysis. It is valid for models 0 and 2. By default, it is 100.