KERNEL: Calculate Kernel Matrix

In SPA3G: SPA3G: R package for the method of Li and Cui (2012)

Description

A function for calculating the kernel matrix using genotype data

Usage

KERNEL(G, weight)

Arguments

G	matrix: genotypes of SNP markers in one gene.
weight	numerical vector: prior weight for each marker

Value

KERNEL function returns a kernel (similarity) matrix.

Examples

## The function is currently defined as
function (G, weight) 
{
    if (length(dim(G)) == 0) {
        size <- length(G)
        k <- matrix(1, size, size)
        for (i in 1:(size - 1)) {
            j <- seq(1, i, 1)
            remain <- G[-j]
            Ones <- matrix(1, length(remain), 1)
            leading <- Ones * G[i]
            D <- abs(remain - leading)
            AM <- D
            AM[AM == 0] <- 4
            AM[AM == 2] <- 0
            AM[AM == 1] <- 2
            AM[remain == 1 & leading == 1] <- 2
            k[i, (i + 1):size] <- k[(i + 1):size, i] <- AM * 
                weight/sum(4 * weight)
        }
    }
    if (length(dim(G)) > 0) {
        size <- nrow(G)
        k <- matrix(1, size, size)
        for (i in 1:(size - 1)) {
            j <- seq(1, i, 1)
            if (i < (size - 1)) {
                remain = as.matrix(G[-j, ])
            }
            if (i == (size - 1)) {
                remain <- t(as.matrix(G[-j, ]))
            }
            Ones <- matrix(1, nrow(remain), 1)
            leading <- Ones %*% G[i, ]
            D <- abs(remain - leading)
            AM <- as.matrix(D)
            AM[AM == 0] <- 4
            AM[AM == 2] <- 0
            AM[AM == 1] <- 2
            AM[remain == 1 & leading == 1] <- 2
            k[i, (i + 1):size] <- k[(i + 1):size, i] <- AM %*% 
                weight/sum(4 * weight)
        }
    }
    return(k)
}

SPA3G documentation built on May 2, 2019, 11:12 a.m.