NAME

SRcompare.pl - Compare a pair of SRmapqtl outut files to see how many cofactors were gained or lost

SYNOPSIS

  SRcompare.pl [-f SRmapqtl.old] [-h] < SRmapqtl.new > output

DESCRIPTION

SRcompare.pl reads from the standard input and writes to the standard output. It is meant to compare the set of cofactors in two SRmapqtl output files. It will print out the number of cofactors that are the same, lost or gained in the two files.

OPTIONS

-f

This option requires an input filename that must exist. It allows the user to specify the old SRmapqtl.out file for processing. If it is not given, then the script dies.

-h

requires no operand. If used, it prints a usage message and exits.

INPUT FILES

The input files should be of the same format as the output of SRmapqtl. You should have only one set of such results in a file to be processed by SRcompare.pl. These results are created by Eqtl as well as SRmapqtl.

OUTPUT

At this time the output will be a single line telling how many cofactors were lost, gained or remained, between the two files. For example:

  10 are the same, 2 were lost and 0 were gained.

Ideally, you would like to see 0 lost and 0 gained.

EXAMPLE

Suppose we have a map in qtlcart.map and a data file in qtlcart.cro, and that there is no resource file in the current directory. For this example, assume that there are only two marker genotypes (that is a backcross or recombinant inbred line) and one trait. The following series of commands can be used to compare the cofactors chosen from interval mapping with those from composite interval mapping:

    % Qstats -X qtlcart
        % Zmapqtl -M 3 -A
        % Eqtl -S 12.0 -H 10 -I Z -A
        % mv qtlcart.z qtlcart.z.1
        % Zmapqtl -M 8 -A
        % mv qtlcart.eqt qtlcart.eqt.1
        % mv qtlcart.sr qtlcart.sr.1
        % Eqtl -S 12.0 -H 10 -I Z -A 
        % SRcompare.pl -f qtlcart.sr.1 < qtlcart.sr

In the above, Qstats is run to set the filename stem. Next, Zmapqtl does an interval mapping analysis and Eqtl picks a set of markers closest to the peaks from interval mapping: These peaks are only used if they have likelihood ratios greater than 12.0. Next, the interval mapping results are moved to an new file and composite interval mapping is run using the cofactors identified via interval mapping. The previous output files of Eqtl (qtlcart.eqt and qtlcart.sr) are renamed and new files are generated from the composite interval mapping results. Then, SRcompare.pl is used to compare the two sets of results, those from interval mapping (qtlcart.sr.1) and those from composite interval mapping (qtlcart.sr).

This type of analysis can be iterated until a stable set of cofactors are identified.

SEE ALSO

Eqtl(1), Qstats(1), SRmapqtl(1), Zmapqtl(1)

AUTHORS

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

        Christopher J. Basten, B. S. Weir and Z.-B. Zeng
        Department of Statistics, North Carolina State University
        Raleigh, NC 27695-7566, USA
        Phone: (919)515-1934