scanTwo | R Documentation |

Evaluate log-likelihood ratio test statistic for epistasis (QTL by QTL interaction).

```
scanTwo(y, x, gdat, prdat = NULL, vc = NULL, numGeno = FALSE,
minorGenoFreq = 0, rmv = TRUE)
```

`y` |
A numeric vector or a numeric matrix of one column (representing a phenotype for instance). |

`x` |
A data frame or matrix, representing covariates if not missing. |

`gdat` |
Genotype data. Should be a matrix or a data frame, with each row representing an observation and each column a marker locus. The column names should be marker names. Optional if an object |

`prdat` |
An object from |

`vc` |
An object from |

`numGeno` |
Whether to treat numeric coding of genotypes as numeric. If true, |

`minorGenoFreq` |
Specify the minimum tolerable minor genotype frequency at a scanning locus if |

`rmv` |
A logical variable. If true, then the scanning locus will be skipped if the minor genotype frequency at the locus is smaller than |

A matrix whose entry in the upper triangle is the log-likelihood test statistic for epistatic effect.

`scanOne`

.

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