R/R2_data_yeast.R

In BayesNetBP: Bayesian Network Belief Propagation

#' Saccharomyces Cerevisiae eQTL data from Kruglak et. al. (2005)
#' 
#' eQTL data from 112 F1 segregants from a cross between BY4716 and 
#' RM11-1a strains of \emph{Saccharomyces Cerevisiae}.
#' 
#' @details 
#' The \code{yeast} dataset is a subset of the widely studied yeast expression 
#' dataset comprising of 112 F1 segregants from a cross between BY4716 and RM11-1a 
#' strains of \emph{Saccharomyces Cerevisiae}. The original dataset consists of 
#' expression values reported as log2(sample/ BY reference) for 6216 genes. 
#' The data can be accessed in Gene Expression Omnibus (GEO) by accession number (GSE1990). 
#' After linkage analysis and filtering based on location and significance of QTL, 
#' a final set of 38 genes and their corresponding 12 SNP markers were identified and 
#' included in the yeast dataset. The gene expression values are discretized around 
#' the median and have two states, 1 (above or equal to median) and -1 (below median). 
#' re are two genotype states: 1 or 2. Thus the final dataset is a data frame of 112 observations 
#' (genotype) of 12 variables (SNP markers) and normalized gene expression of 38 variables (genes).
#' 
#' @format The data set \code{yeast} is a data frame of 112 observations of 50 variables: genotype 
#' data (genotype states at 12 SNP markers) and phenotype data (normalized and discretized 
#' expression values of 38 genes). Both genotypes and phenotypes are of class \code{factor}.

#' @usage data(yeast)
#' @name yeast
#' @docType data
#' 
#' @references 
#' Brem RB, Kruglyak L. The landscape of genetic complexity across 5,700 gene expression traits in yeast. 
#' Proc Natl Acad Sci U S A 2005 Feb 1;102(5):1572-7.\cr
#' \cr
#' Brem RB, Storey JD, Whittle J, Kruglyak L. Genetic interactions between polymorphisms that affect gene 
#' expression in yeast. Nature 2005 Aug 4;436(7051):701-3.
#' 
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