Description Usage Arguments Value

View source: R/scanonevar.meanperm.R

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

1 2 | ```
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)
``` |

`cross` |
An object of class |

`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 |

A vector of length `n.mean.perm`

of the maximum negative log10 p-value that resulted from each permutation.

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