NotationName: Notation of real SNP Name

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

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

NotationName(MaxOrder, SingleEffect, TwoEffect, 
             ThreeEffect, FourEffect, FiveEffect, SNPNames = NA)

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 [e-mail]

References

None

Examples

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

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