geneNetBP (version 1.0.0)

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 contains the following variables:

• yeastgeno

{ a data frame of 112 observations of 9 variables. All column vectors are of class factor} yeastpheno{ a data frame of 112 observations of 16 variables. All column vectors are of class numeric }

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 16 genes and their corresponding 9 SNP markers were identified and included in the yeast dataset.\ Thus the final dataset has 2 variables yeastgeno, data frame of 112 observations (genotype) of 9 variables (SNP markers) and yeastpheno, data frame of 112 observations (normalized gene expression) of 16 variables (genes).\

Examples

# load the data and fit a genotype-phenotype network
data(yeast)
fit.gnbp(yeastgeno,yeastpheno)