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MR_predictor: a simulation engine for Mendelian Randomization studies

2014; Oxford University Press; Volume: 30; Issue: 23 Linguagem: Inglês

10.1093/bioinformatics/btu564

1367-4811

Benjamin F. Voight,

Genetic and phenotypic traits in livestock

Abstract Summary: I present MR_predictor, a simulation engine designed to guide the development and interpretation of statistical tests of causality between phenotypes using genetic instruments. MR_predictor provides a framework to model either individual traits or complex scenarios where multiple phenotypes are correlated or dependent on each other. Crucially, MR_predictor can incorporate the effects of multiple biallelic loci (linked or unlinked) contributing genotypic variability to one or more simulated phenotypes. The software has a range of options for sample generation, and output files generated by MR_predictor port into commonly used analysis tools (e.g. PLINK, R), facilitating analyses germane for Mendelian Randomization studies. Benchmarks for speed and power calculations for summary statistic-based Mendelian Randomization analyses are presented and compared with analytical expectation. Availability and implementation: The simulation engine is implemented in PERL, and the associated scripts can be downloaded from github.com, and online documentation, tutorial and example datasets are available at http://coruscant.itmat.upenn.edu/mr_predictor. Contact: bvoight@upenn.edu Supplementary information: Supplementary derivations are available at Bioinformatics online.