PlotTopEffects: Plot top n effects with their corresponding SNPs or...

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

Description

Effects can be respectively considered as independent effects and combination effects. Independent Effect: Effect that only the SNP or SNP-combination has. Combination Effect: Effect is the addition of all effects of SNP-combination and its sub-combinations. This function plots top n effects (including Independent Effect and Combination Effect) with their corresponding SNPs or SNP-combinations.

Usage

PlotTopEffects(Vertices, Top = 20, SaveFileName = "")

Arguments

Vertices	matrix. Vertices of constructed graphs, including real vertices and virtual vertices. The first column represents SNP ID or SNP-combination ID. The second column represents effect value. The third column represents the class of vertices, "1" -> real vertice, others -> virtual vertice.
Top	numeric. Top n Effects. By default, Top <- 20.
SaveFileName	character. Basic file name for saving figure. By default, SaveFileName <- "".

Value

TopEffect	numeric. Top independent effects of SNPs or SNP-combinations.
CombinationEffect	numeric. Top combination effects of SNPs or SNP-combinations.

Author(s)

Junliang Shang [e-mail]

References

None

Examples

data(Vertices)
data(Edges)
TP <- PlotTopEffects(Vertices, Top = 20, SaveFileName = "")
TopEffect <- TP$TopEffect
CombinationEffect <- TP$CombinationEffect

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