Eqtl reformats the prodigous output of Zmapqtl.
The output file has a section that is suitable for
input to Rcross. There are other sections to the
output that are more readable. Eqtl can also detect whether a
bootstrap, permutation or jackknife analysis was performed and
process the interim files produced by those analyses.
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.
Eqtl uses the specified size (alpha) to determine the significance threshold from the
experiment-wise permutation results. If used, the -S option is ignored, and the
significance threshold is set and saved from the experiment-wise permutation test results.
The size is 0.05 by default.
This should be followed by a string of no more than eight characters. It allows the
user to control which files Eqtl will process. The default is ZM, which means
process the results of Zmapqtl and JZmapqtl (the M is for multitrait). You can
also add the letters P for permutations, B for bootstraps or J for jackknives.
Prior to implementing this option, the default was PBJZM. Note that the order of the
letters indicates the order of processing: If you want to use the threshold from
a permutation test, then the P should precede the Z and M values. Also,
you need to have at least one action.
The input format of the molecular map should be the same as that of the output
format from the program
Rmap. The input format of the individual data should be the same as the output format
of the program
Rcross. The other files should have been created by Zmapqtl. Take care that
Zmapqtl completed its analysis: An incomplete qtlcart.z file can cause
Eqtl to crash.
was used to do a bootstrap experiment or a permutation test, then there will
be interim results files. With the default filename stem and model 3, there
will be files qtlcart.z3c and qtlcart.z3e if a permutation test was done, and
qtlcart.z3a if a bootstrap was done.
Using the work code PBZM will direct Eqtl to
detect these files and processes their results. It will open
a qtlcart.z3e file and determine an experimentwise threshold based on the
size specified with the -a option.
If the qtlcart.z3a file exists, then Eqtl
opens it and computes the means and standard deviations, at each test site,
of the likelihood ratio test statistic, additive effect and dominance effect.
The results are printed to qtlcart.z3b.
The jackknife procedure produces a qtlcart.z3i file. Adding a J to
the work code directs Eqtl to
computes the means and standard deviations
of the likelihood ratio test statistic, additive effect and dominance effect
at each test site.
The results are printed to qtlcart.z3j.
If the resource file indicates that there are more than one
trait, then Eqtl will try to estimate positions and additive effects
for all the traits. This will happen even if no analysis was done on
the extra traits. The output file will then have some null estimates.
When doing a jackknife with
the user should check that the file ending in the letter i is truely the last
version of the interim jackknife file.
switches between a file ending in i and another ending in j, so check both and
move the j file onto the i file if required.
If you set the significance threshold too high, then Eqtl may find no QTL
in the qtlcart.z output. If this is the case, then Eqtl will crash.
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