R/Measure.R2.R

In LDcorSV: Linkage Disequilibrium Corrected by the Structure and the Relatedness

Measure.R2 <- function(biloci, na.presence = TRUE) {
    CALC <- TRUE
    M.r2 <- NA
    
    if (na.presence) {
        if (any(is.na(biloci))) {
            ligne <- na.action(na.omit(biloci))
            # less than 5 non-missing data
            CALC <- (length(ligne) <= (nrow(biloci) - 5))
            if (CALC) { 
                biloci <- biloci[-ligne, ]
            }
        }
    }
    
    if (CALC) {
        SIG <- var(biloci)
        ifelse((SIG[1, 1] < 0.0000001) | (SIG[2, 2] < 0.0000001), 
               M.r2 <- 0, 
               M.r2 <- (SIG[1, 2])^2 / (SIG[1, 1] * SIG[2, 2]))
        as.numeric(M.r2)
    }
    
    M.r2
}