R/f.HWE.design.R

In Haplin: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes

f.HWE.design <- function(data, design, sex){
##
## TESTS EACH LOCUS FOR HWE USING A STANDARD CHI-SQUARED.
## INTENDED ONLY FOR THE GENETIC PART OF THE DATA, WITH STANDARD TRIAD
## STRUCTURE
##

nloci <- length( data$aux$alleles )
data.gen <- data$gen.data
# if(!is.numeric(data)) stop("Data format wrong when testing HWE!")

## ITERATE TESTING OVER LOCI
.ut <- vector( nloci, mode = "list" )
for(i in 1:nloci){
	## FOR EACH LOCUS, STACK MOTHER, FATHER, CHILD AND COMPUTE JOINTLY (IF TRIADS)
	if(design %in% c("triad", "cc.triad")){
		.data.tmp <- data.gen[, ((i-1)*6 + 1):((i-1)*6 + 6)]
		if(missing(sex)){# AUTOSOME TRIAD
			.data.tmp <- rbind(.data.tmp[,1:2], .data.tmp[,3:4], .data.tmp[,5:6])
		}else{# TRIAD ON X-CHROM
			.data.tmp <- rbind(.data.tmp[,1:2], .data.tmp[sex == 2,5:6]) # USES ONLY MOTHERS AND DAUGHTERS
		}
	}
	if(design == "cc"){
		.data.tmp <- data.gen[, ((i-1)*2 + 1):((i-1)*2 + 2)]
		if(!missing(sex)){
			.data.tmp <- .data.tmp[sex == 2,] # USES ONLY GIRLS
		}
	}
	.HWE.test <- f.HWE(.data.tmp, quiet.warning = T)
	.ut[[i]] <- .HWE.test
}


return(.ut)

}