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.

Version: 1.0.4
Depends: R (≥ 3.5.0), SKAT, pedgene, gdsfmt
Imports: AnnotationDbi, DBI, GenomeInfoDb, RSQLite, methods
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, formatR, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
Published: 2018-06-18
Author: Robert V. Baron [aut], Daniel E. Weeks [aut, cre], University of Pittsburgh [cph]
Maintainer: Daniel E. Weeks <weeks at pitt.edu>
BugReports: https://groups.google.com/forum/#!forum/mega2-users
License: GPL-2
URL: https://watson.hgen.pitt.edu/mega2/mega2r/
NeedsCompilation: yes
Materials: NEWS
CRAN checks: Mega2R results

Downloads:

Reference manual: Mega2R.pdf
Vignettes: Mega2R Tutorial
Package source: Mega2R_1.0.4.tar.gz
Windows binaries: r-devel: Mega2R_1.0.4.zip, r-release: Mega2R_1.0.4.zip, r-oldrel: Mega2R_1.0.3.zip
OS X binaries: r-release: Mega2R_1.0.4.tgz, r-oldrel: Mega2R_1.0.3.tgz
Old sources: Mega2R archive

Linking:

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