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. Rcross will overwrite the file if it exists, and create a new file if it does not. If not used, then Rcross will use qtlcart.cro. This output is in a format suitable for any of the mapping programs.

-i

This requires an input filename. This file must exist. Rcross will attempt to identify the format of the file and translate it to another format. Specifying a file with this option turns off the simulation parameters below.

-m

Rcross requires a genetic linkage map. This option require the name of a file containing the map. It should be in the same format that Rmap outputs. The default file is qtlcart.map.

-q

Rcross needs a genetic model to simulate a data set. It will read from the file specified by this option. The file specified should contain a genetic model in the same format as the output of Rqtl. The default file is qtlcart.qtl.

-H

Allows the user to specify the heritability for the trait. If used, it requires a value in the range 0.0 to 1.0. It is 0.5 by default.

-E

Allows the user to specify an environmental variance for the trait. If used, it requires a positive value and will disable the heritability. This is ignored by default.

-I

is the flag to turn on interactive crosses. By default, it has a value of 0. To do interactive crosses, use this option with the value 1.

-c

Allows the user to specify the type of cross. It requires a string such as B1, SF2 or RI1. See below for more on the values of the cross.

-g

This should be used with an integer in the range 0 to 6. It specifies the format of the output. The default is 0 and the other options are defined below.

-n

This is the sample size of the offspring. It is 200 by default and requires some integer value greater than 0 if used.