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

-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

MImapqtl 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 MImapqtl will analyze. If this number is greater than the number of traits, then all traits will be analyzed unless the trait name begins with a minus sign. If a negative number is given, then only traits beginning with a plus sign will be analyzed. The default is to analyze trait 1 only.

-E

Allows the user to specify the name of the file containing the genetic model for input. This file should be in the format of Rqtl.out and produced by Rqtl, Eqtl or MImapqtl. A new model will be placed in the file specified with the -O option. For an initial analysis (phase 0), this will default to qtlcarti.mqt.

-O

Allows the user to specify the name of the file containing the genetic model for output. For an initial analysis (phase 0), this will default to qtlcarto.mqt.

-q

MImapqtl has a limit to the number of QTL it can analyze. For 32 bit machines, this is 19 QTL. For 64 bit machines, this can be 31. If you set this to a number higher than that allowed, it will be reset to the maximum allowed for the machine type.

-k

The user can specify the maximum number of epistatic terms allowed in the model.

-d

MImapqtl walks along an interval at this rate during the refinement of QTL positions and the search for more QTL.

-S

Requires an integer value to indicate the information criterion for declaring the presence or absence of a parameter. Information criteria are explained below.

-L

Requires a real value to indicate the threshold for adding or deleting parameters to a model. Comparisons are made based on the information criterion function specified with the -S option above. The default is 3.84. If this is set too low, the program will continue to find QTL until it hits the upper limit. If set too high, it will not find any QTL.

-I

Requires an eight character string that codes for what the program should do. See below for more explanation.

-p

is used with an integer to specify the phase of the analysis. See below for more explanation.