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

-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

Zmapqtl 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 Zmapqtl 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.

-l

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

-M

Zmapqtl 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 a rate that can be specified with this option. The default is to do an analysis every 2 centiMorgans along the chromosome.

-n

Use this to indicate how many background parameters Zmapqtl uses in composite interval mapping. This is used only with model 6, and gives an upper bound. If fewer than this number of markers are ranked in the SRmapqtl.out file, then less than the specified number of markers will be used.

-w

Zmapqtl 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.

-r

Zmapqtl can do a permutation test to determine the threshold for rejecting the null hypothesis of no QTL at a site. By default, this option sets the number of permutations equal to 0, which means no permutation test is run. You can set it to a number < 10000 to do the test. See Churchill and Doerge (1994) for more details. The results are in an interim file. Use Eqtl to summarize them when enough repetitions have been done. You need to run Zmapqtl without permutations or bootstraps at least once before you can do the permutation tests. This option only allows for interval mapping (Model 3) or composite interval mapping (Model 6).

-b

When used with argument 1, Zmapqtl will do a single bootstrap. You need to run Prune to actually create the bootstrapped data set: This option merely analyzes it and stores summary statistics in an interim file qtlcart.z3b by default, for model 3. You should also run Zmapqtl without bootstraps or permutation tests before doing a bootstrap analysis.

When used with an argument 2, Zmapqtl will do a jackknife analysis. Again, Zmapqtl should be run without this argument prior to doing a jackknife.