BatCINOEDV: Batch mode for using CINOEDV

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

Description

Batch mode for using CINOEDV function.

Usage

BatCINOEDV(FileName, MaxOrder, RatioThreshold, 
           NumberThreshold, measure, Strategy, Population, Iteration, SNPNameFileName)

Arguments

FileName	character. The file name with its format (.mat) that saves SNP data. It has two variables, i.e., pts and class. For pts, Row -> Sample, Column -> SNP, 1 -> AA, 2 -> Aa, 3 -> aa. For class, Row -> 1, Column -> class label, 1 -> case, 2-> control.
MaxOrder	numeric. The considered maximum order of epistatic interactions. It must be setted as 1, 2, 3, 4, or 5.
RatioThreshold	character. It controls the numbers of detected SNPs or SNP-combinations with the help of NumberThreshold. The length of RatioThreshold is equal to MaxOrder. Each element is a decimal in [0,1].
NumberThreshold	character. It controls the numbers of detected SNPs or SNP-combinations with the help of RatioThreshold. The length of NumberThreshold is equal to MaxOrder. Each element is an integer.
measure	numeric. The used evaluation measure. 1 -> the classic co-information measure; 2 -> the normalized co-information measure; 3 -> TingHu's co-informationn measure.
Strategy	The search strategy, 1 -> The exhaustive search strategy, 2 -> The PSO search strategy
Population	numeric. The number of particles. For example, Population=1000.
Iteration	numeric. The number of iterations. For example, Iteration=100.
SNPNameFileName	character. The file name with its format (.mat) that saves the names of SNPs. The file has only one variable, i.e., Name. In Name, Row -> 1, Column -> SNP Name, and the length is equal to RowNum. If not exist such file (default), SNPNameFileName <- NA.

Value

None

Note

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

Author(s)

Junliang Shang [e-mail]

References

None

Examples

File1 <- system.file("extdata","test.mat",package="CINOEDV")
File2 <- system.file("extdata","test1.mat",package="CINOEDV")
File3 <- system.file("extdata","test1_Name.mat",package="CINOEDV")
FileName <- c(File1,File2)
SNFName <- c(NA,File3)
MaxOrder <- 2
RThreshold <- c(1, 1)
NThreshold <- c(10, 10)
measure <- 1
Stra <- 1
Pop <- 10
Iter <- 10
BatCINOEDV(FileName, MaxOrder, RThreshold, NThreshold, measure, Stra, Pop, Iter, SNFName)

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