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
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