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gen.outcomesXtri <- function(na,nb,nc,nm,nf) {
#
# generates all outcomes of tri-allelelic exact test for the X chromosome
#
original.allele.string <- LETTERS[1:3]
Res <- NULL
ma.max <- min(nm,na)
for(ma in ma.max:0) {
mbleft <- min(nm - ma,nb)
for(mb in mbleft:0) {
mc <- min(nm-ma-mb,nc)
aleft <- na-ma
bleft <- nb-mb
cleft <- nc-mc
al.left <- c(aleft,bleft,cleft) # left for females
# print(al.left)
ind <- order(al.left)
al <- original.allele.string[ind]
genotype.string <- c(paste(c(al[1],al[1]),collapse=""),
paste(sort(c(al[1],al[2])),collapse=""),
paste(sort(c(al[1],al[3])),collapse=""),
paste(c(al[2],al[2]),collapse=""),
paste(sort(c(al[2],al[3])),collapse=""),
paste(c(al[3],al[3]),collapse="")) # order of genotypes according to the original minor allele coding
acounts <- al.left[ind] # sorted
Out <- outcomes.3(acounts)
colnames(Out) <- genotype.string
Out <- Out[,c( "AA","AB","AC","BB","BC","CC")] # re-order female genotypes to correspond to original allele coding
if(is.vector(Out)) {
Out <- matrix(Out,nrow=1)
}
nout <- nrow(Out)
Block <- cbind(rep(ma,nout),rep(mb,nout),rep(mc,nout),Out)
Res <- rbind(Res,Block)
}
}
colnames(Res) <- c("A","B","C","AA","AB","AC","BB","BC","CC")
rownames(Res) <- 1:nrow(Res)
return(Res)
}
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