Nothing
LD.clump <- function(x, p, r2.threshold, p.threshold, max.dist = 500e3) {
if(!is(x, "bed.matrix"))
stop("x is not a bed matrix")
if(is.data.frame(p)) {
if(!all(p$chr == x@ped$chr, na.rm = TRUE) | !all(p$pos == x@ped$pos, na.rm = TRUE))
stop("Unmatching SNPs")
a <- p
p <- p$p
} else {
a <- NULL
}
if(length(p) != ncol(x))
stop("Dimensions mismatch")
or <- order(p) - 1L # -1 pour des indices qui démarrent à 0 ds la fction c++
if(!missing(p.threshold)) {
or <- or[ p[or + 1L] < p.threshold ]
if(length(or) == 0) stop("too stringent p.threshold ?")
}
I <- .Call("ld_clump", PACKAGE = "gaston", x@bed, x@mu, x@sigma, r2.threshold, x@snps$pos, x@snps$chr, max.dist, or);
if(is.null(a))
a <- data.frame( chr = x@snps$chr, id = x@snps$id, pos = x@snps$pos, p = p, cluster = I+1)
else {
a$cluster <- I+1
}
a$is.index <- (a$cluster == 1:nrow(a))
a
}
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