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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(CINOEDV)
Loading required package: R.matlab
R.matlab v3.5.1 (2016-03-27) successfully loaded. See ?R.matlab for help.
Attaching package: 'R.matlab'
The following objects are masked from 'package:base':
getOption, isOpen
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: ggplot2
Loading required package: reshape2
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/CINOEDV/NormalizationEffect.Rd_%03d_medium.png", width=480, height=480)
> ### Name: NormalizationEffect
> ### Title: Normalization Effect
> ### Aliases: NormalizationEffect
>
> ### ** Examples
>
>
> data(pts)
> data(class)
> MaxOrder <- 2
> measure <- 1
> SaveFileName <- ""
>
> # Search Strategies
> Effect <- ExhaustiveSearch(pts,class,MaxOrder,measure,0)
Exhaustive Search !
1-order effect computing ...
elapsed
0.045
2-order effect computing ...
elapsed
1.146
> SingleEffect <- Effect$SingleEffect
> TwoEffect <- Effect$TwoEffect
> ThreeEffect <- Effect$ThreeEffect
> FourEffect <- Effect$FourEffect
> FiveEffect <- Effect$FiveEffect
>
> # Normalization
> Effect <- NormalizationEffect(MaxOrder,SingleEffect,TwoEffect,ThreeEffect,FourEffect
+ ,FiveEffect,SaveFileName)
dev.new(): using pdf(file="Rplots24.pdf")
>
> SingleEffect <- Effect$SingleEffect
> TwoEffect <- Effect$TwoEffect
> ThreeEffect <- Effect$ThreeEffect
> FourEffect <- Effect$FourEffect
> FiveEffect <- Effect$FiveEffect
>
>
>
>
>
>
> dev.off()
png
2
>
providing 
.