R/reorder.snp.R

In isglobal-brge/SNPassoc: SNPs-Based Whole Genome Association Studies

`reorder.snp` <-
function(x, ref="common", ...)
{
    s <- x
    if(!inherits(s,"snp")) {
        stop("object must be of class 'snp'")
    }
    
    type <- charmatch(ref, c("common","minor"))
    
    if (is.na(type)) {
        stop("ref must be either 'common' or 'minor'")
    }
    
    class(s) <- "factor"
    tt <- table(s)
    
    if (type==1) {
        if (length(tt) == 3 & min(tt) > 0)  {
            if (tt[1] < tt[3]) {
                s <- relevel(relevel(s, 2), 3)
            } 
        } else {
            if (length(unique(unlist(strsplit(names(tt)[1], "/")))) == 2 
                                                            &  length(tt)>1) {
                s <- relevel(s, 2)
            } 
        }
    } else {
        if (length(tt) == 3 & min(tt) > 0)  {
            if (tt[3] < tt[1]) {
                s <- relevel(relevel(s, 2), 3)
            } 
        } else  {
            if (length(unique(unlist(strsplit(names(tt)[1], "/")))) == 2)  {
                s <- relevel(s, 2)
            } 
        }
    } 
    
    class(s) <- c("snp","factor")
    s
}