R/expandsetupSNP.R

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

`expandsetupSNP` <-
function (o) 
{
	if(!inherits(o,"logical")) { # all missings
        x <- summary(o)
        control <- !is.na(x$allele.freq[,2]) & x$allele.freq[,2] != 0
        o <- order( x$allele.freq[control,2], decreasing = TRUE)
    
        alleles <- rbind(x$allele.names)[o]
        
        if (length(alleles) > 1) {
            alleles <- paste(alleles, collapse = "/")
        }
        
        aux <- ifelse( any(!is.na(x$allele.freq[, 2])),
                       round( max(x$allele.freq[, 2], na.rm = TRUE), 1),
                       NA)
        
        out <- data.frame(alleles = alleles, 
                          major.allele.freq = aux, 
                          HWE = round(x$HWE, 6), 
                          missing = round(x$missing.allele * 100, 1))
        
	} else {
        out <- data.frame(alleles = NA, major.allele.freq = NA, HWE = NA, missing = 100)
    }
    out
}