R: Co-Information based N-Order Epistasis Detector and...
CINOEDV_Main
R Documentation
Co-Information based N-Order Epistasis Detector and Visualizer
Description
This function integrates almost all functions of the package for providing one stop service.
Usage
CINOEDV_Main()
Details
No input parameters
Value
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.
data
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.
results
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.
graphs
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.
Note
The returned values also save in files with (.mat) or (.RData) formats respectively.