qtl Book

#' Rainbow trout doubled haploid data
#'
#' Data from doubled haploid individuals derived from a cross between Oregon
#' State University (OSU) and Clearwater (CW) River rainbow trout clonal lines.
#'
#' Doubled haploid individuals were produced from a cross between Oregon State
#' University (OSU) and Clearwater (CW) river rainbow trout (*Oncorhynchus
#' mykiss*) clonal lines.  Eggs from one of eight outbred females, two from
#' Troutlodge (TL) and six from Spokane (SP), were irradiated to destroy
#' maternal nuclear DNA and fertilized with sperm from a single \eqn{F_1}{F1}
#' male.  The first embryonic cleavage was blocked by heat shock to restore
#' diploidy.  There are a total of 554 individuals, with between 8 and 168
#' individuals from each of the eight females.
#'
#' The primary phenotype is time to hatch (`tth`).  An additional
#' "phenotype", `female`, indicates maternal cytoplasmic environment (the
#' source of the egg).
#'
#' There are genotype data on 171 markers on 28 linkage groups.  The linkage
#' groups are named as in Nichols et al. (2002), though a pair of markers are
#' assigned to linkage group "un", as they don't connect to any of the linkage
#' groups in Nichols et al. (2002).
#'
#' Note that the data have cross type `"dh"` (for doubled haploids); in
#' R/qtl they are treated just like a backcross, except that genotypes are
#' referred to as the homozygotes.
#'
#' @format An object of class `cross`.  See [qtl::read.cross()]
#' for details.
#'
#' @seealso \code{link{gutlength}}, \code{link{iron}}, \code{link{myocard}},
#' \code{link{nf1}}, \code{link{ovar}}
#'
#' @references Nichols, K. M., Broman, K. W., Sundin, K., Young, J. M.,
#' Wheeler, P. A. and Thorgaard, G. H.  (2007) Quantitative trait loci by
#' maternal cytoplasmic environment interaction for development rate in
#' *Oncorhynchus mykiss*. *Genetics* **175**, 335--347.
#'
#' Nichols, K. M., Young, W. P., Danzmann, R. G., Robison, B. D., Rexroad, C.,
#' Noakes, M., Phillips, R. B., Bentzen, P., Spies, I., Knudsen, K., Allendorf,
#' F. W., Cunningham, B. M., Brunelli, J., Zhang, H., Ristow, S., Drew, R.,
#' Brown, K. H., Wheeler, P. A. and Thrgaard, G. H. (2002) A consolidated
#' linkage map for rainbow trout (*Oncorhynchus mykiss*).  *Animal
#' Genetics* **34**, 102--115.
#'
#' @source Krista M. Nichols, Department of Biological Sciences, Purdue
#' University, \email{kmnichol@@purdue.edu}
#'
#' @keywords datasets
#'
#' @examples
#' data(trout)
#' library(qtl)
#' plot(trout)
#'
"trout"