`HDGENE.pruning` <- function(GD=NULL,GM=NULL,block = 10000,LD=0.7){
# Objects: pruning the Genotype based on correlation
# input: GD: m by n matrix
# GM: genotype map information
# block: # of markers considering will have LD
# LD: correlation, above this threshold will be removed
CHR = unique(GM[,2])
SNP.index = NULL
nchr = 0
for(chr in CHR){
index.chr = which(GM[,2]==chr)
GD1 = GD[index.chr,]
SNP.index1 = pruning(GD1,block,LD)
SNP.index1 = SNP.index1 + nchr
SNP.index = append(SNP.index,SNP.index1)
nchr = nchr + length(index.chr)
}
return(SNP.index)
}
`pruning` <- function(GD,block,LD){
m = nrow(GD)
k = ceiling(m/block)
GD1.index = NULL
for( i in 1:k){
down = (i-1) * block + 1
up = i * block
if(up > m) up = m
GD1 = GD[down:up,]
GD.index = Blink.LDRemove(GDneo = GD1, LD=LD, Porder = 1:nrow(GD1),block = 10000, LD.num = 10000)
GD1.index = append(GD1.index,GD.index)
}
return(GD1.index)
}
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