Nothing
compute.bnld <-
function(mpcross1, mpcross2, rmat)
{
output <- list()
nmrk1 <- ncol(mpcross1$founders)
nmrk2 <- ncol(mpcross2$founders)
# pairs of loci
pairs <- expand.grid(1:nmrk1, (nmrk1+1):(nmrk1+nmrk2))
n.pairs <- nrow(pairs)
# order by rows
pairs <- pairs[order(pairs[,1], pairs[,2]), ]
# combine two sets of data
finals <- cbind(mpcross1$id, mpcross1$finals, mpcross2$finals)
founders <- cbind(mpcross1$founders, mpcross2$founders)
pedigree <- mpcross1$pedigree
rpairs <- CR_calcLD(finals, founders, pedigree, pairs, rmat)
output$ld <- list()
output$ld$W <- matrix(data=rpairs[,1], nrow=nmrk1, ncol=nmrk2, byrow=TRUE)
output$ld$LewontinD <- matrix(data=rpairs[,2], nrow=nmrk1, ncol=nmrk2, byrow=TRUE)
output$ld$delta2 <- matrix(data=rpairs[,3], nrow=nmrk1, ncol=nmrk2, byrow=TRUE)
output$ld$r2 <- matrix(data=rpairs[,4], nrow=nmrk1, ncol=nmrk2, byrow=TRUE)
return(output)
}
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