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.

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

Files in this package

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

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