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# TODO adapter pour prendre une liste
bed.merge.inds <- function(x1, x2) {
# on construit ped d'abord
ped <- rbind(x1@ped, x2@ped)
w <- !duplicated( ped[,c("famid", "id")] )
ped <- ped[w,]
w <- order(ped$famid, ped$id)
ped <- ped[w,]
x1_ids <- paste( x1@ped$famid, x1@ped$id, sep = rawToChar(as.raw(10)) ) # newline can't interfer with chars in ids!
x2_ids <- paste( x2@ped$famid, x2@ped$id, sep = rawToChar(as.raw(10)) )
ids <- paste( ped$famid, ped$id, sep = rawToChar(as.raw(10)) )
w1 <- match(ids, x1_ids, 0L)
w2 <- match(ids, x2_ids, 0L)
bed1 <- .Call('gg_extract_inds_indices', x1@bed, w1)
bed2 <- .Call('gg_extract_inds_indices', x2@bed, w2)
bed <- .Call("gg_bind_snps", PACKAGE = "gaston", list(bed1, bed2))
snps <- rbind(x1@snps, x2@snps)
x <- new("bed.matrix", bed = bed, snps = 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(x, verbose = getOption("gaston.verbose", TRUE))
x
}
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