Description Usage Arguments Value Author(s) References Examples
PSO based method for computing main effects of selected SNPs and interaction effects of selected SNP-combinations within the maximum order.
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pts |
matrix. SNP data. Each row represents a sample. Each column represents a SNP. For the element, 1 -> AA, 2 -> Aa, 3 -> aa. |
class |
matrix. Class labels of samples. It only has one row. Each column represents a class label. For the element, 1 -> case, 2-> control. |
MaxOrder |
numeric. The considered maximum order of epistatic interactions. It must be setted as 1, 2, 3, 4, or 5. |
Population |
numeric. The number of particles. For example, Population=1000. |
Iteration |
numeric. The number of iterations. For example, Iteration=100. |
c1 |
numeric. The acceleration factor of individual experience. For example, c1=2. |
c2 |
numeric. The acceleration factor of global experience. For example, c2=2. |
TopSNP |
numeric. The selected SNPs with top indexes. For example, TopSNP=10. |
measure |
numeric. The used evaluation measure. 1 -> the classic co-information measure; 2 -> the normalized co-information measure; 3 -> TingHu's co-informationn measure. |
alpha |
numeric. The lower threshold of effects, either main effects or interaction effects, which must be higher or equal to 0, By default, alpha <- 0. |
SingleEffect |
matrix. main Effects of SNPs. There are 2 columns. The first column saves all SNPs, and the second column saves their corresponding effects. Ddescending save according to their effects. |
TwoEffect |
matrix. interaction Effects of two-SNP combinations. There are three columns. The first two columns save all two-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |
ThreeEffect |
matrix. interaction Effects of three-SNP combinations. There are four columns. The first three columns save all three-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |
FourEffect |
matrix. interaction Effects of four-SNP combinations. There are five columns. The first four columns save all four-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |
FiveEffect |
matrix. interaction Effects of five-SNP combinations. There are six columns. The first five columns save all five-SNP combinations, and the last column saves their corresponding effects. Descending save according to their interaction effects. |
Junliang Shang shangjunliang110@163.com
None
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | data(pts)
data(class)
MaxOrder <- 2
Pop <- 10
Iter <- 10
c1 <- 2
c2 <- 2
TopSNP <- 10
measure <- 1
alpha <- 0
Effect <- PSOSearch(pts, class, MaxOrder, Pop, Iter, c1, c2, TopSNP, measure, alpha)
SingleEffect <- Effect$SingleEffect
TwoEffect <- Effect$TwoEffect
ThreeEffect <- Effect$ThreeEffect
FourEffect <- Effect$FourEffect
FiveEffect <- Effect$FiveEffect
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