This function is a wrapper from the GWASpoly package that creates the incidence matrix to be used when calculating the -log10 scores for the markers once the variance components and marker effects are estimated.

1 | ```
design.score(Mi,model,ploidy,min.MAF,max.geno.freq)
``` |

`Mi` |
marker to be used |

`model` |
model to be used for designing the matrix. The default is "additive" which can be extend to any ploidy level but alternative models for polyploids such as "additive","1-dom-alt","1-dom-ref","2-dom-alt","2-dom-ref" are supported based on Rosyara (2016) |

`ploidy` |
A numeric value indicating the ploidy level of the organism. The default is 2 which means diploid but higher ploidy levels are supported. |

`min.MAF` |
minimum minor allele frequency |

`max.geno.freq` |
1 - min.MAF |

- $S
an incidence matrix for the marker based on the model provided.

The core function of the package `mmer`

1 | ```
# it works internally in the \code{\link{mmer}} function
``` |

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