setMethod("initialize", "Trio", function(.Object, ... ){
.Object <- callNextMethod()
.Object
})
setMethod("GeneDrop", signature( trio = "Trio", geno.vec = "numeric"), function( trio, geno.vec ){
g1 <- geno.vec[trio@id]
g2 <- geno.vec[trio@spouse]
for (i in 1:length(trio@offspring)){
if( is.character(trio@offspring[[i]]) ){
if( is.na(geno.vec[ trio@offspring[[i]]])){
goff <- gene.drop.fn(g1,g2)
geno.vec[ trio@offspring[[i]] ] <- goff
}
}else{
# this is the case where the offspring is a trio object
if( is.na(geno.vec[ trio@offspring[[i]]@id])){
goff <- gene.drop.fn(g1,g2)
geno.vec[ trio@offspring[[i]]@id ] <- goff
geno.vec <- GeneDrop(trio@offspring[[i]], geno.vec)
}
}
}
return( geno.vec )
})
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