Mega2R: Accessing and Processing a 'Mega2' Genetic Database

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 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.

Package details

AuthorRobert V. Baron [aut], Daniel E. Weeks [aut, cre], University of Pittsburgh [cph]
MaintainerDaniel E. Weeks <[email protected]>
LicenseGPL-2
Version1.0.4
URL https://watson.hgen.pitt.edu/mega2/mega2r/
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("Mega2R")

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Mega2R documentation built on June 19, 2018, 1:01 a.m.