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The Mega2R package: R tools for accessing and processing genetic data in common formats.

Robert V Baron1, Justin R Stickel1, Daniel E Weeks1,2

  • 1Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, USA.

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|March 5, 2019
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Summary
This summary is machine-generated.

Mega2 and Mega2R streamline genetic data reformatting for over 40 analysis programs, enhancing linkage and association studies. Mega2R efficiently loads compressed genetic data into R, simplifying gene-based association tests.

Keywords:
Mega2RSQLitedatabasegene-based association testsgenome-wide association studiesgenotypeslinkagephenotypes

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Area of Science:

  • Genetics and Bioinformatics
  • Computational Biology
  • Statistical Genetics

Background:

  • Genetic data reformatting is crucial for linkage and association analyses.
  • Existing tools often lack support for diverse genetic data formats and analysis programs.

Purpose of the Study:

  • To introduce Mega2, a C++ program for genetic data reformatting.
  • To present Mega2R, an R package for efficient data loading and analysis.
  • To enhance gene-based association testing workflows.

Main Methods:

  • Mega2 converts data from formats like PLINK, VCF, BCF, and IMPUTE2.
  • Utilizes a SQLite database for intermediate data representation.
  • Mega2R loads Mega2 SQLite databases into R, employing memory-efficient compressed genotype storage.

Main Results:

  • Mega2 supports over 40 linkage and association analysis programs.
  • Mega2R facilitates gene-based tests, including family-based and SKAT analyses.
  • Mega2R enhances GenABEL by supporting additional input formats (PLINK, VCF, IMPUTE2).

Conclusions:

  • Mega2 and Mega2R provide a robust and flexible solution for genetic data management.
  • These open-source tools simplify complex genetic analyses, improving accessibility and efficiency.
  • The integrated workflow supports a wide range of genetic research applications.