NAME

Emap - Infer a genetic linkage map from data

SYNOPSIS

Emap [ -i data input ] [ -o data output ] [ -m map input ] [ -l map output ] [ -S s size ] [ -L l size ] [ -M method [ -r permutations ] [ -f map function ] [ -p parameter ] [ -O obj. function ]

DESCRIPTION

Emap infers a genetic linkage map from a data set. It uses the rapid chain delineation method of Doerge and Weir.

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

Use this to specify the data output file. Emap will overwrite the file if it exists, and create a new file if it does not. The default value is qtlcart.cro.

-i

You need to specify a data input file with this option. The data should be Rcross.out, cross.inp or mapmaker.raw format.

-m

Use this to specify the map input file. Emap will read the map from this file and try to rearrange markers to improve their ordering.

-l

The completed map will be written to a file specified with this option. The default is qtlcart.map.

-M

Requires an integer to indicate the linkage map method. At present, the only options are 10, 11, 12 or 13.

-f

Requires an integer option to specify the mapping function. See Rmap(1) for more information on mapping functions.

-p

Requires a real number. Some map functions need an extra parameter, and this allows the user to specify it. See the manual for details.

-S

This allows you to specify the significance level for declaring segregation distortion between a pair of markers.

-L

This allows you to specify the significance level for declaring linkage between a pair of markers.

-r

This allows you to specify the number of permutations. It is not an active option at this time.

-O

This allows you to specify the objective function. Use 0 for SAL (sum of adjacent likelihoods) or 1 for SAR (sum of adjacent recombination fractions).

INPUT FORMAT

Emap recognizes three types of files. The first is the Rcross.out format. The second is a special format defined in the example file cross.inp included in the distribution. Finally, MAPMAKER raw files can be read by Emap.

EXAMPLES

        % Emap -i sample.raw

Will attempt to create a genetic linkage map for the data in the sample.raw file.

REFERENCES

Doerge, R.W. and B. S. Weir (1999) . XXX 1, 174-181.

BUGS

This is an initial version and needs some work. It does fine on simulated data, but could use some testing with real data.

SEE ALSO

Emap(1), Rmap(1), Rqtl(1), Rcross(1), Qstats(1), LRmapqtl(1), BTmapqtl(1), SRmapqtl(1), JZmapqtl(1), Eqtl(1), Prune(1), Preplot(1), MImapqtl(1), MultiRegress(1), Examples(1) SSupdate.pl(1), Prepraw.pl(1), EWThreshold.pl(1), GetMaxLR.pl(1), Permute.pl(1), Vert.pl(1), CWTupdate.pl(1), Ztrim.pl(1), SRcompare.pl(1), Ttransform.pl(1), TestExamples.pl(1), Model8.pl(1), Dobasics.pl(1), Bootstrap.pl(1)

CONTACT INFO

In general, it is best to contact us via email (zeng@statgen.ncsu.edu)

        Christopher J. Basten, B. S. Weir and Z.-B. Zeng
        Bioinformatics Research Center, North Carolina State University
        1523 Partners II Building/840 Main Campus Drive
        Raleigh, NC 27695-7566     USA
        Phone: (919)515-1934

Please report all bugs via email to qtlcart-bug@statgen.ncsu.edu.

The QTL Cartographer web site ( http://statgen.ncsu.edu/qtlcart ) has links to the manual, man pages, ftp server and supplemental materials.