Notation of real SNP Name

Description

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.

Usage

1
2

Arguments

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

Value

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.

Author(s)

Junliang Shang shangjunliang110@163.com

References

None

Examples

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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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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