yeast: Yeast cis-QTL Gene Regulatory Network Dataset

In sparseSEM: Elastic Net Penalized Maximum Likelihood for Structural Equation Models with Network GPT Framework

Yeast cis-QTL Gene Regulatory Network Dataset

Description

The dataset (Y,X) are two matrices each with 3380 rows and 112 columns as described in the Vignettee "Elastic Net Enabled Sparse-Aware Maximum Likelihood for Structural Equation Models in Inferring Gene Regulatory Networks".

The Yeast expression trait data set was obatained from Brem R.B. and Kruglyak L (2005), and has been screened through:
1. screen and keep the ORF names in Kellis's ORF list (Kellis M et al, 2003);
2. screen out ORF with more than 5% of missing expression date;
3. perform eQTL mapping by Wilcoxon test, adjust by qvalue; keep the top one cisQTL;
4. fill in zeros for ORF without cisQTL in matrix X

Usage

data(yeast)

Format

The format is matrix.

Details

Yeast cis-QTL Gene Regulatory Network Dataset

References

1. Brem RB, Kruglyak L: 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 2005, 102:1572-1577.
2. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254

Examples

data(yeast)

sparseSEM documentation built on Aug. 9, 2023, 5:07 p.m.