An alternative way to do the permutation test is in a batch file. For composite interval mapping, one might want to reselect the background markers with SRmapqtl in each permutation. To this end, one would need to permute the traits, reselect the background markers and then run the composite interval mapping. The pseudo code example in Section 2.4.2 shows how to do this without the SRmapqtl step.
In the bootstrap, new datasets are created from the original by sampling with replacement. New datasets are the same size as the original. The statistics are redone and printed out. See the section Prune as to how to do bootstrapping.
Jackknife resampling is performed by calculating (the sample size) new estimates of the parameters: The th estimate is calculated by deleting individual from the dataset. The standard deviation over these new estimates provides an estimate of the standard deviation for the test statistic and additive and dominance effects. You invoke the Jackknife by setting the number of bootstraps to 2. Zmapqtl uses two interim files to perform the jackknife. If you are using Model 6 in Zmapqtl and your filename stem is qtlcart, then these files will be called qtlcart.z6i and qtlcart.z6j. These files contain the sum and sum of squares up to the previous and current iteration, as Zmapqtl runs. Initially, the qtlcart.z6i file contains columns of zeros: This is the sum before any iterations are performed. Subsequently, qtlcart.z6j will contain the interim state after each odd-numbered iteration, while qtlcart.z6i will contain the state after each even-numbered iteration. If individual has no trait data, then the th iteration will be skipped. For this reason, one cannot be sure that the file ending in ``j'' is the last iteration for odd sample sizes. It is best to look at both files at the conclusion of a jackknife experiment, and rename the interim file with the greater number of iterations to qtlcart.z6i. It this is done, then Eqtl will recognize it and calculate the means and sample standard deviations of the test statistic and effects.
To clarify the interim file names, we consider an example using Model 6 in Zmapqtl and the default filename stem ``qtlcart''. Table 3.5 lists the interim file names. Eqtl automatically looks for files named qtlcart.z6e, qtlcart.z6a and qtlcart.z6i. These files will be processed and the appropriate calculations done. Eqtl will overwrite the qtlcart.z6b and qtlcart.z6j files after completing its calculations, so if you want to save them, do so before running Eqtl. If you chose to use another model (say model 3), then the ``6'' in the filenames of Table 3.5 would be a ``3''.