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################################################################################
# Convert the genotype data from A,C,G,T format to A, H, B, N.
# Daniel Gatti
# Dan.Gatti@jax.org
# Arguments: geno: character matrix with genotypes. Sample IDs in rownames
# & SNP IDs in colnames. num.samples x num.SNPs.
################################################################################
convert.genotypes = function(geno) {
# Get the alleles for each SNP.
tbl = apply(geno, 2, table)
# Remove the no-calls for the moment. We'll deal with them below.
tbl = lapply(tbl, function(a) { a[names(a) != "-"] })
# Count the number of alleles.
tbl.len = sapply(tbl, length)
# If we do not have more than 3 alleles, stop.
if(max(tbl.len) > 4) {
stop("The number of alleles at some SNPs is greater than 4.")
} # if(max(tbl.len) > 4)
# Process the single allele genotypes first.
ss = which(tbl.len == 1)
geno[,ss] = matrix("A", nrow(geno), length(ss), byrow = TRUE)
# Process two allele genotypes.
ss = which(tbl.len == 2)
alleles = sapply(tbl[ss], names)
for(i in 1:ncol(alleles)) {
if(alleles[1,i] %in% c("AA", "CC", "GG", "TT")) {
geno[geno[,ss[i]] == alleles[1,i], ss[i]] = "A"
if(alleles[2,i] %in% c("AA", "CC", "GG", "TT")) {
geno[geno[,ss[i]] == alleles[2,i], ss[i]] = "B"
} else {
geno[geno[,ss[i]] == alleles[2,i], ss[i]] = "H"
} # else
} else {
geno[geno[,ss[i]] == alleles[1,i], ss[i]] = "H"
geno[geno[,ss[i]] == alleles[2,i], ss[i]] = "A"
} # else
} # for(i)
# Process three allele genotypes.
ss = which(tbl.len == 3)
alleles = sapply(tbl[ss], names)
for(i in 1:ncol(alleles)) {
geno[geno[,ss[i]] == alleles[1,i], ss[i]] = "A"
geno[geno[,ss[i]] == alleles[2,i], ss[i]] = "H"
geno[geno[,ss[i]] == alleles[3,i], ss[i]] = "B"
} # for(i)
# Replace the missing data symbol with = "N".
geno[geno == "-"] = "N"
return(geno)
} # convert.genotypes()
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