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########################### rbind
bed_rbind <- function(..., deparse.level = 1) {
L <- list(...)
M <- lapply(L, function(x) x@snps)
# ici il faudrait faire un truc un peu plus fin ... (plutôt vérifier chr:pos:alleles...)
if(!all_eq( lapply(M, function(x) x$id)))
stop("SNP ids are not identical, can't bind matrices")
common_colnames <- Reduce(intersect, lapply(L, function(x) colnames(x@ped)))
ped <- Reduce(rbind, lapply(L, function(x) x@ped[common_colnames]))
if(anyDuplicated(ped[, c("famid", "id")]))
warning("There are duplicated individuals (same family and individual id)")
a <- .Call("gg_alleles_recoding", PACKAGE = "gaston", M)
M <- lapply(L, function(x) x@bed)
bed <- .Call("gg_bind_inds2", PACKAGE = "gaston", M, a$flip)
x <- new("bed.matrix", bed = bed, snps = L[[1]]@snps, ped = ped,
p = NULL, mu = NULL, sigma = NULL,
standardize_p = FALSE, standardize_mu_sigma = FALSE )
if(getOption("gaston.auto.set.stats", TRUE))
x <- set.stats.snps(x, verbose = FALSE)
if(a$swap_reference > 0)
warning(a$swap_reference, " reference allele inversions were performed during binding")
if(a$flip_strand > 0)
warning(a$flip_strand, " allele strand flips were performed during binding")
if(a$NAs > 0)
warning(a$NAs, " SNPs were set to NA because alleles were incompatibles")
x
}
setGeneric("rbind", signature="...")
setMethod("rbind", signature=c(...="bed.matrix"), definition = bed_rbind)
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