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 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.

Package details

AuthorRobert V. Baron [aut], Daniel E. Weeks [aut, cre], University of Pittsburgh [cph]
Bioconductor views Genetics
MaintainerDaniel E. Weeks <weeks@pitt.edu>
LicenseGPL-2
Version1.1.0
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")

Try the Mega2R package in your browser

Any scripts or data that you put into this service are public.

Mega2R documentation built on May 29, 2024, 1:14 a.m.