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

Share:

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.

Author
Junliang Shang
Date of publication
2014-11-27 09:45:12
Maintainer
Junliang Shang <shangjunliang110@163.com>
License
GPL-2
Version
2.0

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