qtl Book

#' Interspecific backcross in Drosophila
#'
#' Data on ovariole number in a backcross between *D. simulans* and
#' *D. sechellia*; the majority of individuals were selected to be
#' recombinant in the region of a putative QTL on chromosome 3.
#'
#' The data come from an interspecific Drosophila backcross.  *D.
#' simulans* was crossed to *D. sechellia*, and the \eqn{F_1}{F1} hybrid
#' was crossed back to *D. simulans*.
#'
#' The phenotype of interest was ovariole number in females (a measure of
#' fitness).  Phenotypes `on1` and `on2` are the ovariole counts in
#' the left and right gonads.  The phenotype `onm` is the average of the
#' two counts; for many individuals, the ovariole count for one of two gonads
#' was missing, and so `onm` is missing.
#'
#' In an initial cross of 402 individuals, 383 had complete phenotype data.
#' Initial genotyping focused on 94 individuals with extreme phenotype.
#'
#' To increase the resolution of a major QTL identified on chromosome 3, a
#' second cross of approximately 7000 flies was performed, though only 1050
#' individuals showing a recombination event between two morphological markers,
#' *st* (bright red eyes) and *e* (dark brown body), were phenotyped
#' and genotyped; 1038 had complete phenotype data.  The aim was to oversample
#' recombinants of the region of the QTL.
#'
#' There are genotype data for 24 markers on 3 chromosomes.  (The fourth
#' chromosome had one marker, but showed no effect and is not included in these
#' data.)
#'
#' The phenotype `cross` indicates whether an individual came from the
#' first or second cross.
#'
#' Alleles `"I"` and `"E"` refer to *D. simulans* and *D.
#' sechellia*, respectively.
#'
#' @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{trout}}
#'
#' @references Orgogozo, V., Broman, K. W. and Stern, D. L.  (2006)
#' High-resolution QTL mapping reveals sign epistasis controlling ovariole
#' number between two Drosophila species. *Genetics* **173**, 197--205.
#'
#' @source Virginie Orgogozo, Department of Ecology and Evolutionary Biology,
#' Princeton University, \email{virginie.orgogozo@@normalesup.org}
#'
#' @keywords datasets
#'
#' @examples
#' data(ovar)
#' library(qtl)
#' plot(ovar)
#'
"ovar"