期刊
BIOINFORMATICS
卷 32, 期 10, 页码 1479-1485出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btv722
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资金
- European Commission SYSCOL FP7
- European Research Council
- Louis Jeantet Foundation
- Swiss National Science Foundation
- SystemsX
- NIH-NIMH (GTEx)
- Helse Sor Ost
Motivation: In order to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing. Results: We have developed FastQTL, a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of permutations is modeled using beta distributions trained from a few permutations and from which adjusted P-values can be estimated at any level of significance with little computational cost. The Geuvadis & GTEx pilot datasets can be now easily analyzed an order of magnitude faster than previous approaches.
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