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

Detecting and visualizing nonlinear interaction effects of single nucleotide polymorphisms or epistatic interactions, especially high-order epistatic interactions, are important topics in bioinformatics because of their significant mathematical and computational challenges. We present CINOEDV (Co-Information based N-Order Epistasis Detector and Visualizer) for detecting, visualizing, and analyzing high-order epistatic interactions by introducing virtual vertices into the construction of a hypergraph. CINOEDV was developed as an alternative to existing software to build a global picture of epistatic interactions and unexpected high-order epistatic interactions, which might provide useful clues for understanding the underlying genetic architecture of complex diseases.

Install the latest version of this package by entering the following in R:
install.packages("CINOEDV")
AuthorJunliang Shang
Date of publication2014-11-27 09:45:12
MaintainerJunliang Shang <shangjunliang110@163.com>
LicenseGPL-2
Version2.0

View on CRAN

Man pages

BatCINOEDV: Batch mode for using CINOEDV

CheckVerticeType: Test Vertice Type

CINOEDV_Main: Co-Information based N-Order Epistasis Detector and...

CINOEDV-package: Co-Information based N-Order Epistasis Detector and...

class: Class labels of samples

CoInformation: Co-Information Computation

CombinationEntropy: Combination Entropy Computation

ConstructCompleteGraph: Construct complete graph

DegreeAnalysis: Degree analysis of real vertices

Edges: Edges of constructed graphs

EvaluationMeasure: Evaluation Measure

ExhaustiveSearch: Exhaustive Search

FiveEffect: Interaction Effects of five-SNP combinations

FourEffect: Interaction Effects of four-SNP combinations

HeatMapFactor: Heatmap function

InputData: Input data

InstallPackage: Install CINOEDV used packages

NetworkData: Collect vertices and edges for network construction

NormalizationEffect: Normalization Effect

NotationName: Notation of real SNP Name

PlotTopEffects: Plot top n effects with their corresponding SNPs or...

PSOSearch: PSO Search

pts: SNP data

SingleEffect: Main Effects of SNPs

SubgraphSplit: Split subgraphs

TestMaxOrder: Test the parameter MaxOrder

TestNumberThreshold: Test the parameter NumberThreshold

TestPSOParameters: Check the PSO parameters

TestRatioThreshold: Test the parameter RatioThreshold

TestSNPNameFile: Test the parameter TestSNPNameFile

ThreeEffect: Interaction Effects of three-SNP combinations

tic: Start stopwatch timer

toc: Read elasped time from stopwatch

TwoEffect: Interaction Effects of two-SNP combinations

Vertices: Vertices of constructed graphs

Functions

BatCINOEDV Man page
CheckVerticeType Man page
CINOEDV Man page
CINOEDV_Main Man page
CINOEDV-package Man page
class Man page
CoInformation Man page
CombinationEntropy Man page
ConstructCompleteGraph Man page
DegreeAnalysis Man page
Edges Man page
EvaluationMeasure Man page
ExhaustiveSearch Man page
FiveEffect Man page
FourEffect Man page
HeatMapFactor Man page
InputData Man page
InstallPackage Man page
NetworkData Man page
NormalizationEffect Man page
NotationName Man page
PlotTopEffects Man page
PSOSearch Man page
pts Man page
SingleEffect Man page
SubgraphSplit Man page
TestMaxOrder Man page
TestNumberThreshold Man page
TestPSOParameters Man page
TestRatioThreshold Man page
TestSNPNameFile Man page
ThreeEffect Man page
tic Man page
toc Man page
TwoEffect Man page
Vertices Man page

Files

inst
inst/extdata
inst/extdata/dat100.mat
inst/extdata/test_Name.mat
inst/extdata/test.mat
inst/extdata/test1_Name.mat
inst/extdata/test1.mat
NAMESPACE
data
data/Vertices.rda
data/class.rda
data/pts.rda
data/TwoEffect.rda
data/SingleEffect.rda
data/FourEffect.rda
data/Edges.rda
data/FiveEffect.rda
data/ThreeEffect.rda
R
R/PlotTopEffects.R R/TestSNPNameFile.R R/TestPSOParameters.R R/NetworkData.R R/TestRatioThreshold.R R/TestNumberThreshold.R R/SubgraphSplit.R R/CoInformation.R R/NotationName.R R/tic.R R/PSOSearch.R R/InstallPackage.R R/DegreeAnalysis.R R/CheckVerticeType.R R/CINOEDV_Main.R R/toc.R R/ExhaustiveSearch.R R/ConstructCompleteGraph.R R/CombinationEntropy.R R/InputData.R R/NormalizationEffect.R R/BatCINOEDV.R R/TestMaxOrder.R R/HeatMapFactor.R R/EvaluationMeasure.R
MD5
DESCRIPTION
man
man/TwoEffect.Rd man/TestSNPNameFile.Rd man/FiveEffect.Rd man/NormalizationEffect.Rd man/TestNumberThreshold.Rd man/CINOEDV_Main.Rd man/Vertices.Rd man/toc.Rd man/CoInformation.Rd man/ThreeEffect.Rd man/class.Rd man/CINOEDV-package.Rd man/ConstructCompleteGraph.Rd man/CombinationEntropy.Rd man/tic.Rd man/InputData.Rd man/pts.Rd man/NotationName.Rd man/CheckVerticeType.Rd man/SingleEffect.Rd man/TestPSOParameters.Rd man/FourEffect.Rd man/PlotTopEffects.Rd man/HeatMapFactor.Rd man/BatCINOEDV.Rd man/NetworkData.Rd man/PSOSearch.Rd man/DegreeAnalysis.Rd man/ExhaustiveSearch.Rd man/TestMaxOrder.Rd man/TestRatioThreshold.Rd man/SubgraphSplit.Rd man/EvaluationMeasure.Rd man/Edges.Rd man/InstallPackage.Rd

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Please suggest features or report bugs with the GitHub issue tracker.

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