Mega2R-package: Mega2R: Accessing and Processing a 'Mega2' Genetic Database
In Mega2R: Accessing and Processing a 'Mega2' Genetic Database
Mega2R-package R Documentation
Mega2R: Accessing and Processing a 'Mega2' Genetic Database
Description
Uses as input genetic data that have been reformatted and stored in a 'SQLite' database; this database is initially created by the standalone 'mega2' C++ program (available freely from https://watson.hgen.pitt.edu/register/). Loads and manipulates data frames containing genotype, phenotype, and family information from the input 'SQLite' database, and decompresses needed subsets of the genotype data, on the fly, in a memory efficient manner. We have also created several more functions that illustrate how to use the data frames as well as perform useful tasks: these permit one to run the 'pedgene' package to carry out gene-based association tests on family data using selected marker subsets, to run the 'SKAT' package to carry out gene-based association tests using selected marker subsets, to run the 'famSKATRC' package to carry out gene-based association tests on families (optionally) and with rare or common variants using selected marker subsets, to output the 'Mega2R' data as a VCF file and related files (for phenotype and family data), and to convert the data frames into CoreArray Genomic Data Structure (GDS) format.
Author(s)
Maintainer: Daniel E. Weeks weeks@pitt.edu
Authors:
Robert V. Baron rvb5@pitt.edu
Other contributors:
University of Pittsburgh [copyright holder]
See Also
Useful links:
Mega2R documentation built on May 29, 2024, 1:14 a.m.
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| Mega2R-package | R Documentation |
Mega2R: Accessing and Processing a 'Mega2' Genetic Database
Description
Uses as input genetic data that have been reformatted and stored in a 'SQLite' database; this database is initially created by the standalone 'mega2' C++ program (available freely from https://watson.hgen.pitt.edu/register/). Loads and manipulates data frames containing genotype, phenotype, and family information from the input 'SQLite' database, and decompresses needed subsets of the genotype data, on the fly, in a memory efficient manner. We have also created several more functions that illustrate how to use the data frames as well as perform useful tasks: these permit one to run the 'pedgene' package to carry out gene-based association tests on family data using selected marker subsets, to run the 'SKAT' package to carry out gene-based association tests using selected marker subsets, to run the 'famSKATRC' package to carry out gene-based association tests on families (optionally) and with rare or common variants using selected marker subsets, to output the 'Mega2R' data as a VCF file and related files (for phenotype and family data), and to convert the data frames into CoreArray Genomic Data Structure (GDS) format.
Author(s)
Maintainer: Daniel E. Weeks weeks@pitt.edu
Authors:
Robert V. Baron rvb5@pitt.edu
Other contributors:
University of Pittsburgh [copyright holder]
See Also
Useful links:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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