Description Usage Arguments Value Note Author(s) References Examples
Batch mode for using CINOEDV function.
1 2 | BatCINOEDV(FileName, MaxOrder, RatioThreshold,
NumberThreshold, measure, Strategy, Population, Iteration, SNPNameFileName)
|
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. |
None
The returned values save in files with (.mat) or (.RData) formats respectively.
Junliang Shang shangjunliang110@163.com
None
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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)
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