title: kruX: matrix-based non-parametric eQTL discovery.
abstract: BACKGROUND
  The Kruskal-Wallis test is a popular non-parametric statistical test for identifying expression quantitative trait loci (eQTLs) from genome-wide data due to its robustness against variations in the underlying genetic model and expression trait distribution, but testing billions of marker-trait combinations one-by-one can become computationally prohibitive.
  
  
  RESULTS
  We developed kruX, an algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at once. KruX is more than ten thousand times faster than computing associations one-by-one on a typical human dataset. We used kruX and a dataset of more than 500k SNPs and 20k expression traits measured in 102 human blood samples to compare eQTLs detected by the Kruskal-Wallis test to eQTLs detected by the parametric ANOVA and linear model methods. We found that the Kruskal-Wallis test is more robust against data outliers and heterogeneous genotype group sizes and detects a higher proportion of non-linear associations, but is more conservative for calling additive linear associations.
  
  
  CONCLUSIONS
  kruX enables the use of robust non-parametric methods for massive eQTL mapping without the need for a high-performance computing infrastructure and is freely available from http://krux.googlecode.com.
authors.forename: Jianlong
authors.initials: J
authors.lastname: Qi
authors.forename: Hassan Foroughi
authors.initials: HF
authors.lastname: Asl
authors.forename: Johan
authors.initials: J
authors.lastname: Björkegren
authors.affiliation: School of Life Sciences - LifeNet, Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany. tom.michoel@roslin.ed.ac.uk.
authors.forename: Tom
authors.initials: T
authors.lastname: Michoel
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016678:Genome / Q000235:genetics; D005838:Genotype; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D015203:Reproducibility of Results; D012984:Software; D018709:Statistics, Nonparametric