Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
By Andrey Shabalin,
Department of Biostatistics,
University of North Carolina at Chapel Hill
... just shortened my computing time from a year to a couple of days
Adaikalavan Ramasamy, Ph.D., King's College London
Official tool of the GTEx project
Please cite as:
Shabalin, A.A. Matrix eQTL: Ultra fast eQTL analysis via large matrix operations. Bioinformatics 28, no. 10 (2012): 1353-1358.
- Designed for eQTL analysis of large datasets.
- Performs testing for each transcript-SNP pair.
- Ultra fast without loss of precision.
- Equally fast for models with covariates.
- Linear additive and ANOVA models.
Includes tests for genotype-covariate
- Covariates to account for sex, population structure, surrogate variables, etc.
- Correlated and heteroskedastic errors.
- Correction for multiple testing using FDR .
- Separate FDR for cis- and trans- eQTLs (more info).
- Convenient R package.
|Matrix eQTL, Matlab
|Matrix eQTL, Rev R
|Matrix eQTL, R+GOTO
Info: Details of the testing procedure.
Fact: Matrix eQTL results match those from other software.
Comparison conducted analyzing CF dataset with 573,337 SNPs and 22,011 transcripts over 840 samples.
Tested on a quad-core PC, using additive linear models with zero and with 10 covariates.
Getting started with Matrix eQTL
Features of Matrix eQTL
Manuscript in Bioinformatics (2012)
Questions, comments, concerns?
Contact me: Andrey A. Shabalin
Support Matrix eQTL
- 2013, September 3 mdash; Huge update. Version 2.0.0
- Half of the code and most of the manual/website rewritten.
- Added effect sizes to the output.
- Added option to record best p-value for each gene/SNP regardless of p-value threshold.
- Added option to turn off FDR calculation and write output file in the process, not at the end.
- Fixed FDR calculation for trans tests (small difference in q-values).
- Fixed: Gene-SNP pairs are local if the distance between them is less or equal to cisDist (was a strict comparison before).
- Included toy data set in the package (less than 3kb).
- Previous updates
By Andrey Shabalin