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 ). 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.