If there are real SNP names which will be used for constructing graphs and further analysis, this function then replaces SNP indexes by real SNP names.

1 2 | ```
NotationName(MaxOrder, SingleEffect, TwoEffect,
ThreeEffect, FourEffect, FiveEffect, SNPNames = NA)
``` |

`MaxOrder` |
numeric. The considered maximum order of epistatic interactions. It must be setted as 1, 2, 3, 4, or 5. |

`SingleEffect` |
matrix. main Effects of SNPs. There are 2 columns. The first column saves all SNPs, and the second column saves their corresponding effects. Ddescending save according to their effects. |

`TwoEffect` |
matrix. interaction Effects of two-SNP combinations. There are three columns. The first two columns save all two-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |

`ThreeEffect` |
matrix. interaction Effects of three-SNP combinations. There are four columns. The first three columns save all three-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |

`FourEffect` |
matrix. interaction Effects of four-SNP combinations. There are five columns. The first four columns save all four-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |

`FiveEffect` |
matrix. interaction Effects of five-SNP combinations. There are six columns. The first five columns save all five-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |

`SNPNames` |
character or logical (NA). Names of SNPs. Row -> 1, Column -> SNP Name |

`SingleEffect` |
matrix. main Effects of SNPs. There are 2 columns. The first column saves all SNPs, and the second column saves their corresponding effects. Ddescending save according to their effects. |

`TwoEffect` |
matrix. interaction Effects of two-SNP combinations. There are three columns. The first two columns save all two-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |

`ThreeEffect` |
matrix. interaction Effects of three-SNP combinations. There are four columns. The first three columns save all three-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |

`FourEffect` |
matrix. interaction Effects of four-SNP combinations. There are five columns. The first four columns save all four-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |

`FiveEffect` |
matrix. interaction Effects of five-SNP combinations. There are six columns. The first five columns save all five-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |

Junliang Shang shangjunliang110@163.com

None

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | ```
data(pts)
data(class)
MaxOrder <- 2
measure <- 1
SaveFileName <- ""
SNPNames <- c("rs1366208","rs1950123","rs10485136","rs1484673",
"rs1484433","rs1795462","rs10501558","rs2018041",
"rs10489495","rs3846302","rs2801008","0","rs1773409",
"rs4786670","rs2260614","rs1326298","rs9315726",
"rs1582545","rs10505084","rs4763023")
# Search Strategies
Effect <- ExhaustiveSearch(pts,class,MaxOrder,measure,0)
SingleEffect <- Effect$SingleEffect
TwoEffect <- Effect$TwoEffect
ThreeEffect <- Effect$ThreeEffect
FourEffect <- Effect$FourEffect
FiveEffect <- Effect$FiveEffect
# Normalization
Effect <- NormalizationEffect(MaxOrder,SingleEffect,TwoEffect,ThreeEffect,FourEffect
,FiveEffect,SaveFileName)
SingleEffect <- Effect$SingleEffect
TwoEffect <- Effect$TwoEffect
ThreeEffect <- Effect$ThreeEffect
FourEffect <- Effect$FourEffect
FiveEffect <- Effect$FiveEffect
# SNP Name Notation
Effect <- NotationName(MaxOrder,SingleEffect,TwoEffect,ThreeEffect,FourEffect
,FiveEffect,SNPNames)
SingleEffect <- Effect$SingleEffect
TwoEffect <- Effect$TwoEffect
ThreeEffect <- Effect$ThreeEffect
FourEffect <- Effect$FourEffect
FiveEffect <- Effect$FiveEffect
``` |

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