geneNetBP (version 2.0.1)

yeast: Saccharomyces Cerevisiae eQTL data from Kruglak et. al. (2005)

Description

eQTL data from 112 F1 segregants from a cross between BY4716 and RM11-1a strains of Saccharomyces Cerevisiae.

Usage

data(yeast)

Format

The data set 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 factor.

Source

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.\ 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.\

Details

The 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 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). There 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).\

Examples

## Not run: 
# # load the data and fit a genotype-phenotype network
# data(yeast)
# fit.dbn(yeast[,1:12],yeast[,13:50])
# ## End(Not run)