R: Permutation test for mean effect in scanonevar

scanonevar.meanperm {qtl} | R Documentation

## Permutation test for mean effect in scanonevar

### Description

Executes permutations of the genotypes in the mean-effect part of scanonevar

### Usage

    scanonevar.meanperm(cross, pheno.col=1, mean_covar=NULL, var_covar=NULL,
               maxit=25, tol=1e-6, n.mean.perm = 2, seed = 27517, quiet=TRUE)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`pheno.col` | 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.
`mean_covar` | Numeric matrix with covariates affecting the mean.
`var_covar` | Numeric matrix with covariates affecting the variances.
`maxit` | Maximum number of iterations in the algorithm to fit the model at a given position.
`tol` | Tolerance for convergence.
`n.mean.perm` | Numeric vector of length one indicates the number of permutations to execute.
`seed` | Numeric vector of length one indicates the random seed to start the permutations.
`quiet` | If `FALSE`, print some information about the course of the calculations.

### Value

A vector of length `n.mean.perm` of the maximum negative log10 p-value that resulted from each permutation.

[Package qtl version 1.41-6 Index]