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

Description Usage Details Value Note Author(s) References Examples

View source: R/CINOEDV_Main.R


This function integrates almost all functions of the package for providing one stop service.




No input parameters



list. It returns six parameters, including FileName, MaxOrder, RatioThreshold, NumberThreshold, SNPNameFileName, and measure. FileName: character. The file name with its format (.mat) that saves SNP data. MaxOrder: numeric. The considered maximum order of epistatic interactions. RatioThreshold: numeric. It controls the numbers of detected SNPs or SNP-combinations with the help of NumberThreshold. NumberThreshold: numeric. It controls the numbers of detected SNPs or SNP-combinations with the help of RatioThreshold. SNPNameFileName: character or logical (NA). The file name with its format (.mat) that saves the names of SNPs. measure: numeric. The used evaluation measure.


list. It returns used data, including pts, class, and SNPNames. pts: matrix. SNP data. class: matrix. Class labels of samples. SNPNames: character or logical (NA). Names of SNPs.


list. It returns detected results, including SingleEffect, TwoEffect, ThreeEffect, FourEffect, and FiveEffect. SingleEffect: matrix. main Effects of SNPs. TwoEffect: matrix. interaction Effects of two-SNP combinations. ThreeEffect: matrix. interaction Effects of three-SNP combinations. FourEffect: matrix. interaction Effects of four-SNP combinations. FiveEffect: matrix. interaction Effects of five-SNP combinations.


list. It returns observed results from the constructed graph, including Edges, Vertices, TopEffect, Degrees, SubgraphSNPs, CombinationEffect and HeatMapFactors. Edges: matrix. Edges of constructed graphs. Vertices: matrix. Vertices of constructed graphs, including real vertices and virtual vertices. TopEffect: numeric. Top independent effects of SNPs or SNP-combinations. Degrees: matrix. Degrees of real vertices. SubgraphSNPs: list. SNPs in each subgraph of the graph. CombinationEffect: numeric. Top combination effects of SNPs or SNP-combinations. HeatMapFactors: data.frame. The heatmap data for observing how a SNP or a SNP-combination influencing the phenotype.


The returned values also save in files with (.mat) or (.RData) formats respectively.


Junliang Shang [email protected]




# See details of package CINOEDV

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