Executes permutations of the genotypes in the variance-effect part of scanonevar
scanonevar.varperm(cross, pheno.col=1, mean_covar=NULL, var_covar=NULL,
maxit=25, tol=1e-6, n.var.perm = 2, seed = 27517, quiet=TRUE)A vector of length n.var.perm of the maximum negative log10 p-value that resulted from each permutation.
An object of class cross. See
read.cross for details.
Column number in the phenotype matrix which should be used as the phenotype. This must be a single value (integer index or phenotype name) or a numeric vector of phenotype values, in which case it must have the length equal to the number of individuals in the cross, and there must be either non-integers or values < 1 or > no. phenotypes; this last case may be useful for studying transformations.
Numeric matrix with covariates affecting the mean.
Numeric matrix with covariates affecting the variances.
Maximum number of iterations in the algorithm to fit the model at a given position.
Tolerance for convergence.
Numeric vector of length one indicates the number of permutations to execute.
Numeric vector of length one indicates the random seed to start the permutations.
If FALSE, print some information about the course
of the calculations.