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. JZmapqtl will append the file if it exists, and create a new file if it does not. If not used, then JZmapqtl will use qtlcart.zj, where the j indicates the trait analyzed and the zero'th file contains joint mapping.

-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

JZmapqtl 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 JZmapqtl 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 results from Eqtl. JZmapqtl reads those results and uses the information to choose cofactors for some of the analysis methods.

-S

Allows the user to specify the name of the file containing results from SRmapqtl. JZmapqtl reads the results and uses the information to choose cofactors for composite interval mapping model 6.

-M

JZmapqtl assumes the specified model (see below) in the analysis. Model 3 is default.

-c

The user can specify a specific chromosome for Zmapqtl to analyze. If zero, then all will be analyzed.

-d

Zmapqtl walks along the chromosome at this rate. The default is to do an analysis every 2 centiMorgans along the chromosome.

-n

Use this to limit the number of background parameters that JZmapqtl uses in composite interval mapping. This is used only with model 6. It tells JZmapqtl to use markers with rank no higher than specified with this option. Markers are ranked by SRmapqtl.out and only those markers for traits in the analysis with sufficient rank are used.

-w

JZmapqtl blocks out a region of this many centiMorgans on either side of the markers flanking the test position when picking background markers. It is 10 by default and is only used in models 5 and 6. We refer to it as the window size.

-I

JZmapqtl requires the user to specify which hypotheses to test. For backcrosses, there are two hypotheses numbered 1 and 0. Use 10 for backcrosses or a 14 to do GxE tests as well. For crosses in which there are three genotypic classes, there are hypotheses 0, 1, 2, and 3. Use 30, 31, 32 in that case or 34 to do GxE. These are explained in greater detail in the manual.