README.md

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