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.
