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.
| Version: |
1.1.0 |
| Depends: |
R (≥ 3.5.0), SKAT, pedgene, gdsfmt |
| Imports: |
AnnotationDbi, DBI, GenomeInfoDb, RSQLite, methods, famSKATRC, kinship2 |
| LinkingTo: |
Rcpp |
| Suggests: |
knitr, rmarkdown, formatR, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db |
| Published: |
2023-12-21 |
| DOI: |
10.32614/CRAN.package.Mega2R |
| 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 |
Documentation:
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