PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships

Meyer, H. V., Birney, E. (September 2018) PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships. Bioinformatics, 34 (17). pp. 2951-2956. ISSN 1367-4803

URL: https://www.ncbi.nlm.nih.gov/pubmed/29617944
DOI: 10.1093/bioinformatics/bty197

Abstract

Motivation: Simulation is a critical part of method development and assessment. With the increasing sophistication of multi-trait and multi-locus genetic analysis techniques, it is important that the community has flexible simulation tools to challenge and explore the properties of these methods. Results: We have developed PhenotypeSimulator, a comprehensive phenotype simulation scheme that can model multiple traits with multiple underlying genetic loci as well as complex covariate and observational noise structure. This package has been designed to work with many common genetic tools both for input and output. We describe the underlying components of this simulation tool and illustrate its use on an example dataset. Availability and implementation: PhenotypeSimulator is available as a well documented R/CRAN package and the code is available on github: https://github.com/HannahVMeyer/PhenotypeSimulator. Supplementary information: Supplementary data are available at Bioinformatics online.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > annotation > phenotyping
CSHL Authors:
Communities: CSHL labs > Meyer Lab
Depositing User: Matthew Dunn
Date: 1 September 2018
Date Deposited: 25 Mar 2019 14:36
Last Modified: 25 Mar 2019 14:36
PMCID: PMC6129313
Related URLs:
URI: http://repository.cshl.edu/id/eprint/37742

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