dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis

Chao Ye; Bo Jiang; Xuegong Zhang; Jun S Liu

doi:10.1093/bioinformatics/btv021

dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis

Bioinformatics. 2015 Jun 1;31(11):1842-4. doi: 10.1093/bioinformatics/btv021. Epub 2015 Jan 20.

Authors

Chao Ye¹, Bo Jiang¹, Xuegong Zhang², Jun S Liu²

Affiliations

¹ MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China, Department of Statistics, Harvard University, Cambridge, MA 02138, USA, School of Life Sciences, Tsinghua University, Beijing 100084, China and Center of Statistics, Tsinghua University, Beijing 100084, China.
² MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China, Department of Statistics, Harvard University, Cambridge, MA 02138, USA, School of Life Sciences, Tsinghua University, Beijing 100084, China and Center of Statistics, Tsinghua University, Beijing 100084, China MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China, Department of Statistics, Harvard University, Cambridge, MA 02138, USA, School of Life Sciences, Tsinghua University, Beijing 100084, China and Center of Statistics, Tsinghua University, Beijing 100084, China.

PMID: 25609796
DOI: 10.1093/bioinformatics/btv021

Abstract

Many statistical problems in bioinformatics and genetics can be formulated as the testing of associations between a categorical variable and a continuous variable. A dynamic slicing method was proposed for non-parametric dependence testing, which has been demonstrated to have higher powers compared with traditional methods such as Kolmogorov-Smirnov test. We introduce an R package dslice to facilitate the use of dynamic slicing method in bioinformatic applications such as quantitative trait loci study and gene set enrichment analysis.

Availability and implementation: dslice is implemented in Rcpp and available in the Comprehensive R Archive Network. The package is distributed under the GNU General Public License (version 2 or later).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Computational Biology / methods
Gene Expression*
Genetic Variation
Humans
Mice
Phenotype
Quantitative Trait Loci*
Software*
Statistics, Nonparametric