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

Description

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

Usage

1

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.

Author(s)

Junliang Shang [email protected]

References

None

Examples

1
# See details of package CINOEDV

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