gtex: GTEx data

In flashier: Empirical Bayes Matrix Factorization

GTEx data

Description

Derived from data made available by the Genotype Tissue Expression (GTEx) project (Lonsdale et al. 2013), which provides z-scores for assessing the significance of effects of genetic variants (single nucleotide polymorphisms, or SNPs) on gene expression across 44 human tissues. To reduce the data to a more manageable size, Urbut et al. (2019) chose the "top" SNP for each gene — that is, the SNP associated with the largest (absolute) z-score over all 44 tissues. This yields a 16,069 \times 44 matrix of z-scores, with rows corresponding to SNP-gene pairs and columns corresponding to tissues. The dataset included here is further subsampled down to 1000 rows.

Format

gtex is a matrix with 1000 rows and 44 columns, with rows corresponding to SNP-gene pairs and columns corresponding to tissues.

Source

<https://github.com/stephenslab/gtexresults/blob/master/data/MatrixEQTLSumStats.Portable.Z.rds>

References

Lonsdale et al. (2013). "The Genotype-Tissue Expression (GTEx) project." Nature Genetics 45(6), 580–585.

Urbut, Wang, Carbonetto, and Stephens (2019). "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions." Nature Genetics 51(1), 187–195.

Examples

data(gtex)
summary(gtex)

flashier documentation built on Oct. 17, 2023, 5:07 p.m.