Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
By Andrey Shabalin,
... 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
Used by seeQTL browser
Basis of Multiple Tissue eQTL
Please cite R package
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 all or only local transcript-SNP pair.s
- Ultra-fast, no loss of precision.
- Equally fast for models with covariates.
- Linear additive and ANOVA models. Supports testing for the effect of genotype-covariate interaction.
- Covariates to account for sex, population structure, surrogate variables, etc.
- Correlated and heteroskedastic errors.
- Correction for multiple testing using FDR .
- Separate p-value thresholds and FDR control for local and distant eQTLs (more info).
- Convenient R package at CRAN Repository .
|Matrix eQTL, Matlab
|Matrix eQTL, Rev R
|Matrix eQTL, R+GOTO
Info: Details of the testing procedure.
Fact: Matrix eQTL results match those by 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.
Manuscript in Bioinformatics (2012)
Getting started with Matrix eQTL
Features of Matrix eQTL
Frequently Asked Questions
Questions, comments, concerns?
Contact me: Andrey A. Shabalin
Support Matrix eQTL
- 2014, February 24 — Update. Version 2.1.0
- Added support for more than 3 ANOVA categories (see
- Added option to reduce memory consumption for large gene data sets.
- Faster cis-only analysis. Much faster for small
cisDist and small slice sizes.
- File names for the output can now also be connections or
- Redesign of QQ-plots.
plot function now follows the R convention and uses
ylim instead of
- Fixed a bug occurring for genes collinear with covariates.
- Removed extra space in the output header (for linear models with beta estimates)
pvbins are now fixed for QQ-plots. This makes aggregation of results easier.
- Previous updates