NormalizationEffect: Normalization Effect

In CINOEDV: Co-Information based N-Order Epistasis Detector and Visualizer

Description

Normalization of main effects, and n-order interaction effects in SingleEffect, TwoEffect, ThreeEffect, FourEffect and FiveEffect respectively.

Usage

NormalizationEffect(MaxOrder, SingleEffect, TwoEffect, 
                    ThreeEffect, FourEffect, FiveEffect, SaveFileName = "")

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.
SaveFileName	character. Basic file name for saving figure. By default, SaveFileName <- "".

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 [e-mail]

References

None

Examples

data(pts)
data(class)
MaxOrder <- 2
measure <- 1
SaveFileName <- ""
 
# 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

CINOEDV documentation built on May 29, 2017, 9:07 p.m.