R/seagull_data.R

In seagull: Lasso, Group Lasso, and Sparse-Group Lasso for Mixed Models

#' @title A simulated data set to get quickly started
#' 
#' @description This data set contains a genotype matrix, phenotype vectors for
#' three traits (stored in a matrix with three columns) and a vector of groups.
#' The data resembles a sample of a dairy cattle population. The sample includes
#' 1000 individuals and 466 genotypes. For the simulation, a mixed model without
#' fixed effects was used.
#' 
#' @name seagull_data
#' 
#' @docType data
#' 
#' @author Jan Klosa \email{klosa@fbn-dummerstorf.de}
#' 
#' @format A data set which is based on 1000 individuals and 466 explanatory
#' variables.
#' \describe{
#'   \item{genotypes}{a genotype matrix that contains information from single
#'   nucleotide polymorphisms (SNPs). Dimensions are 1000 rows, 466 columns. The
#'   data was simulated using the software
#'   \href{https://alphagenes.roslin.ed.ac.uk}{AlphaSim} of which an R-package
#'   is available. Each row corresponds to a single individual. 1000 individuals
#'   were simulated, where 10 half sib families were created. Each family
#'   consists of 100 half sibs. The half sibs share a common Sire. 466 SNPs are
#'   available, distributed over 2 chromosomes to an equal amount, i.e., the
#'   first 233 SNPs are located on chromosome 1, the remaining SNPs are on the
#'   second chromosome. The complementary homozygote genotypes are coded as 0
#'   and 2, respectively. The heterozygote genotype as 1.}
#'   \item{groups}{a vector of integers which assigns each variable (genotype
#'   marker) to a particular group. The clustering was performed via the R
#'   package \href{http://www.math-evry.cnrs.fr/publications/logiciels}{BALD}.
#'   This package uses linkage disequilibrium as a measure of proximity. In
#'   total, 98 groups are available. Group sizes vary from 1 to 23. The median
#'   of group sizes is equal to 3. For more details about the distribution of
#'   the group sizes, please check out the example on this page:
#'   \code{\link[seagull]{groups}}.}
#'   \item{phenotypes}{a matrix consisting of 1000 rows and 3 columns. Each row
#'   corresponds to a different individual. Each column corresponds to a
#'   different trait. The different traits were simulated to be uncorrelated to
#'   one another. The trait in the first, second, and third column have a
#'   heritability equal to 0.1, 0.3, and 0.5, respectively.}
#' }
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