aksarkar / gtex-fqtl

Factored QTL analysis applied to GTEx and GWAS of 114 complex traits

Factored QTL analysis on GTEx v6p data

Results of Sarkar and Park et al. (2017) submitted.

Results

All the tissue and SNP effect sizes can be bound in

result/stat/chr1/50/combined.txt.gz

(...)

result/stat/chr22/50/combined.txt.gz

Note that individual by tissue gene expression matrix Y was regressed on cis-regulatory genotype matrix X with factored effect size matrix.

Y ~ X * sum_k (Theta[, k] * t(Theta[, k])) + confounders + errors

Each row contains

1. ENSEMBL.ID : unique gene ID
2. Chromosome : chromosome name (1 to 22)
3. TSS : transcription start site (provided by GTEx v6p)
4. Tissue.idx : comma-separate tissue indexes
5. Tissue.names : comma-separate tissue names
6. Tissue.theta : comma-separate tissue effect sizes
7. Tissue.se : comma-separate tissue effect size standard errors
8. Tissue.lodds : comma-separate tissue PIP log-odds
9. SNP.names : comma-separate SNP names
10. SNP.theta : comma-separate SNP effect sizes
11. SNP.se : comma-separate SNP effect size standard errors
12. SNP.lodds : comma-separate SNP PIP log-odds
13. k : factor index
14. pip : posterior inclusion probability cutoff