R/feather2calc_genoprob.R

In byandell/qtl2feather: Feather Database for R/qtl2 Genotype Probabilities

# feather_genoprob
#' Store genotype probabilities in feather database
#'
#' Uses package feather to convert R object created in R/qtl2 for fast access.
#'
#' @param object Object of class \code{\link{feather_genoprob}}.
#'
#' @return An object of class \code{\link[qtl2]{calc_genoprob}}.
#'
#' @details
#' The genotype probabilities are extracted from 1-2 feather databases. Each chromosome is extracted in turn.
#'
#' @export
#' @keywords utilities
#'
#' @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 <- feather_genoprob(probs, "grav2", dir)
#' nprobs <- feather2calc_genoprob(fprobs)
#'
feather2calc_genoprob <- function(object) {
  if(!inherits(object, "feather_genoprob"))
    stop("object must inherit class feather_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]]

  class(result) <- attrs$class[-1]

  result
}