In this directory, we provide all the instructions for reproducing the GTEx results from: “Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions” (Urbut et al 2017).

Figure 3:Summary of primary patterns identified by mash in GTEx data

Figure 5:Histogram of Sharing

Figure 6:Pairwise sharing by magnitude of eQTL among tissues

Supplementary Figure 1:Sample sizes and effective sample sizes from mash analysis across tissues

Supplementary Figure 2:There are 4 figures here:

Summary of covariance matrices Uk with largest estimated weight (> 1%) in GTEx data:Uk2

Summary of covariance matrices Uk with largest estimated weight (> 1%) in GTEx data:Uk4

Summary of covariance matrices Uk with largest estimated weight (> 1%) in GTEx data:Uk5

Summary of covariance matrices Uk with largest estimated weight (> 1%) in GTEx data:Uk8

Supplementary Figure 3: Illustration of how Linkage Disequilibrium can impact effect estimate table and figure

Supplementary Figure 4:Pairwise Sharing By Sign

Supplementary Figure 5:Number of “tissue-specific eQTLs” in each tissues.

Supplementary Figure 6:Expression levels in genes with “tissue-specific eQTLs” are similar to those in other genes

Table 1: Heterogeneity Analysis Simulation and Data.