Nothing
########################### remove duplicated
SNP.rm.duplicates <- function(x, by = "chr:pos", na.keep = TRUE, incomp.rm = TRUE) {
if (!is(x, "bed.matrix")) stop("x should be a bed.matrix")
b <- strsplit(by,':')[[1]]
if ('alleles' %in% b) b <- c(b[b!='alleles'], 'A1', 'A2')
# where are duplicated SNPs
dupli <- SNP.match(x@snps[,b,drop=FALSE], x@snps[SNP.duplicated(x, by=by),], by = by)$index
a <- .Call("gg_alleles_duplicated", PACKAGE = "gaston", x@snps, dupli)
if (incomp.rm) w <- which(a$keep == TRUE)
else w <- which(is.na(a$keep) | a$keep == TRUE)
bed <- .Call("gg_duplicated_remove", PACKAGE = "gaston", x@bed, dupli, a$keep, a$swap_reference, length(w), na.keep, incomp.rm)
new <- new("bed.matrix", bed = bed, snps = x@snps[w,], ped = x@ped,
p = NULL, mu = NULL, sigma = NULL,
standardize_p = FALSE, standardize_mu_sigma = FALSE )
if(getOption("gaston.auto.set.stats", TRUE))
new <- set.stats.snps(new, verbose = FALSE)
w <- sum(a$swap_reference)
if(w > 0)
warning(w, " reference allele inversions were performed to remove duplicated SNP")
w <- sum(a$flip_strand)
if(w > 0)
warning(w, " allele strand flips were performed to remove duplicated SNP")
if(a$NAs > 0)
{
if (incomp.rm) warning(a$NAs, " duplicated SNPs were removed because their alleles were incompatible")
else warning(a$NAs, ' duplicated SNPs have incompatible alleles. Use "SNP.duplicated" function to identify them.')
}
new
}
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