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# fst_extract (previously fst2calc_genoprob)
#' Extract genotype probabilities from fst database
#'
#' Extract genotype probabilities from fst database as an ordinary calc_genoprob object.
#'
#' @param object Object of class `"fst_genoprob"`, linking to an fst database of genotype probabilities.
#'
#' @return An object of class `"calc_genoprob"` (a list of 3-dimensional arrays).
#'
#' @details
#' The genotype probabilities are extracted from the fst database. Each chromosome is extracted in turn.
#'
#' @export
#' @keywords utilities
#' @seealso [fst_genoprob()]
#'
#' @examples
#' library(qtl2)
#' grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
#' map <- insert_pseudomarkers(grav2$gmap, step=1)
#' probs <- calc_genoprob(grav2, map, error_prob=0.002)
#' dir <- tempdir()
#' fprobs <- fst_genoprob(probs, "grav2", dir, overwrite=TRUE)
#' nprobs <- fst_extract(fprobs)
#'
#' # clean up: remove all the files we created
#' unlink(fst_files(fprobs))
fst_extract <-
function(object)
{
if(!inherits(object, "fst_genoprob"))
stop("object must inherit class fst_genoprob")
attrs <- attributes(object)
chr <- unclass(object)$chr
result <- vector(mode = "list", length = length(chr))
names(result) <- chr
for(chri in chr)
result[[chri]] <- object[[chri]]
# Set up attributes.
ignore <- match(c("names","class"), names(attrs))
for(a in names(attrs)[-ignore])
attr(result, a) <- attrs[[a]]
# strip off fst_genoprob from class
cl <- attrs$class
class(result) <- cl[cl != "fst_genoprob"]
result
}
#' @describeIn fst_extract Deprecated version (to be deleted)
#' @export
fst2calc_genoprob <-
function(object)
{
warning("fst2calc_genoprob() is deprecated and will be removed; use fst_extract() instead.")
fst_extract(object)
}
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