yeast: Yeast Genetical Genomics Data

In BigSEM: Constructing Large Systems of Structural Equations

Description

A set of data from a genetical genomics experiment on yeast, including 112 observations on 722 gene expression levels and 732 genotypic values.

Usage

data("yeast")

Format

A list with two data frames and one list.

geneexp

expression levels of of 722 genes.

snps

genotypic values of 732 SNPs.

ciseqtl

a list of the indices of cis-eQTL for each gene.

Details

The experiment included 112 segregants from a cross between two strains BY4716 and RM11-la (Brem and Kruglyak, 2005). The data here only keep 722 genes which have marginally significant cis-eQTL (p-value < 0.05). The set of cis-eQTL for each gene was filtered to control a pairwise correlation under 0.90, and then further filtered to keep up to three cis-eQTL which have the strongest association with the corresponding gene expression.

Source

Brem, R. B. and Kruglyak, L. (2005) The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proceedings of the National Academy of Sciences of the United States of America, 102(5):1572-1577.

References

Chen, C., Zhang, M., and Zhang, D. (2016) A Two-Stage Penalized Least Squares Method for Constructing Large Systems of Structural Equations. (Submitted)

Examples

data(yeast)
summary(yeast)
attach(yeast)

#yeastsem <- fitsem(y=geneexp,x=snps,sk=ciseqtl)

Example output

        Length Class      Mode
geneexp 722    data.frame list
snps    732    data.frame list
ciseqtl 722    -none-     list

BigSEM documentation built on May 2, 2019, 3:37 p.m.