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Zmapqtl outputs a great deal of information: Often the experimenter will want a quick summary of the positions and effects of the QTLs. The program Eqtl scans the output of Zmapqtl and reformats it. Part of the output of Eqtl is identical to the output format of Rqtl. This is convenient if the experimenter would like to do simulation studies with a set of estimated QTLs. The output of Eqtl can be used as the input to Rcross (with the appropriate genetic linkage map), and new data sets can be simulated to examine the power of the different methods to detect the QTLs. Finally, the output of Eqtl can be read by Zmapqtl and used to create virtual markers to be used as covariates in composite interval mapping (see model seven of Section 3.4.2).

The remaining output is more readable and is appropriate if the experimenter is not interested in doing further simulations. The positions of the QTL are given in Morgans from the telomere rather than recombination frequencies from the flanking markers.

Eqtl also appends some output to the SRmapqtl.out file. Once putative QTL are identified, Eqtl determines which markers are closest to these QTL and writes them to the SRmapqtl.out file. These markers will be in a table similar to the output of SRmapqtl itself. They can be read by Zmapqtl when running model 8.

In addition to reformatting the output of Zmapqtl, Eqtl will automatically detect whether a permutation test, jackknife or bootstrap experiment had been done. If such results exist, Eqtl will open and summarize them. For example, if you do a permutation test with Zmapqtl using interval mapping, an interim file qtlcart.z3e is created and appended to for each permutation. Eqtl will read this file and calculate experimentwise threshold values from it. Standard significance thresholds will be written to the log file. The user can specify a type I error rate (size) and Eqtl will calculate a threshold value relevant to it. Once done, the threshold value will be remembered and used by subsequent runs of Eqtl or Preplot.

For bootstrap results from Zmapqtl using interval mapping, Eqtl looks for a file qtlcart.z3a. If found, Eqtl will read in the sums and sums of squares of the likelihood ratio, additive effect and dominance effect at each position and print the mean and sample standard deviations into a summary file (qtlcart.z3d). Eqtl does similar calculations for the jackknife results that would be in qtlcart.z3i.

Table 4.1 shows the command line options specific to Eqtl.

Table 4.1: Command Line Options for Eqtl
Option Default Explanation
-z qtlcart.z (Composite) Interval Mapping Results
-o qtlcart.eqt Output File
-m Genetic Linkage Map File
-M 3 Model from Zmapqtl
-H 10 Hypothesis Test (10,14,30,31,32,34)
-S 10.0 Significance threshold
-a 0.05 Size ($\alpha$)
-L 0 Output LOD scores? (0=no,1=yes)
-I ZM Work Code

next up previous contents index
Next: Options Up: Visualization of Results Previous: Visualization of Results   Contents   Index
Christopher Basten 2002-03-27