An algorithm for multiple quantitative trait locus (QTL) scan with epistatic interactions. PruneDIRECT algorithm has specific strengths for permutation testing. It has been integrated to a flexible, parallel computing framework for identifying multiple interacting QTL which uses the map-reduce model as implemented in Hadoop. This framework is implemented in R, a widely used software tool among geneticists. This enables users to rearrange algorithmic steps to adapt genetic models, search algorithms, and parallelization steps to their needs in a flexible way.

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PruneDIRECT classification

PruneDIRECT specifications

Software type:
Package
Restrictions to use:
None
License:
GNU General Public License version 3.0
Stability:
Stable
Source code URL:
https://github.com/PruneDIRECT/RVersion.git
Interface:
Command line interface
Programming languages:
R
Computer skills:
Advanced

Publications

  • (Mahjani et al., 2016) A flexible computational framework using R and Map-Reduce for permutation tests of massive genetic analysis of complex traits. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
    PMID: 26887003

PruneDIRECT support

Maintainer

Credits

Institution(s)

Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden; Helsinki Institute of Physics, University of Helsinki, Helsinki, Finland; Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

Link to literature

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