Nothing
# find columns in a genotype probability array that should be dropped
#
# Xonly: If TRUE and probs is a list, just look at the X chromosome
genoprobs_col2drop <-
function(probs, Xonly=TRUE, tol=1e-8)
{
if(is.list(probs)) { # proper calc_genoprob object, hopefully
is_x_chr <- attr(probs, "is_x_chr")
if(Xonly) {
result <- lapply(seq_len(length(probs)), function(a) numeric(0))
names(result) <- names(probs)
if(is.null(is_x_chr) || !any(is_x_chr)) return(result) # no X chr
w <- which(is_x_chr)
for(i in w)
result[[i]] <- genoprobs_col2drop(probs[[i]])
return(result)
}
else {
result <- lapply(seq_len(length(probs)), function(a) numeric(0))
names(result) <- names(probs)
for(i in seq_len(length(probs)))
result[[i]] <- genoprobs_col2drop(probs[[i]])
return(result)
}
}
# put genotypes first and take rowMeans
wh <- which(rowMeans(aperm(probs, c(2,1,3))) < tol)
names(wh) <- NULL # eliminate names
wh
}
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