Nothing
CR_gen_geno <-
function(map, map.function, ped, seed, transpos, transval)
{
genome <- combine_chr(map, map.function)
genome2 <- genome
if (transval>0)
genome2[transpos] <- 0
num.loci <- length(genome)+1
# select row numbers of founders in pedigree
indx <- which(ped[,2]==0 & ped[,3]==0)
n.founders <- length(indx)
genC <- .C("gengeno", as.double(genome), as.double(genome2), as.integer(ped[,1]), as.integer(ped[,2]), as.integer(ped[,3]), as.integer(num.loci), as.integer(n.founders), as.integer(nrow(ped)), as.integer(seed), as.integer(transpos[1]-1), as.integer(transval-1), out=integer(length=nrow(ped)*(num.loci*2)), PACKAGE="mpMap")
# convert genC results into sim.data
sim.data <- matrix(data=genC$out, nrow=nrow(ped), ncol=2*num.loci, byrow=TRUE)
colnames(sim.data) <- c(paste("ibd1_", names(unlist(map)), sep=""),
paste("ibd2_", names(unlist(map)), sep=""))
geno <- list()
# make sure that sim.data has the correct elements - founders, finals, etc.
geno$founders <- sim.data[1:n.founders,1:ncol(sim.data)]
geno$finals <- sim.data[ped[,4]==1, 1:ncol(sim.data)]
geno$id <- ped[ped[,4]==1,1]
geno$fid <- ped[indx,1]
geno$pedigree <- ped
geno$map <- map
return(geno)
}
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