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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 |
| Reference manual: | Mega2R.pdf |
| Vignettes: |
Mega2R Tutorial |
| Package source: | Mega2R_1.1.0.tar.gz |
| Windows binaries: | r-devel: Mega2R_1.1.0.zip, r-release: Mega2R_1.1.0.zip, r-oldrel: Mega2R_1.1.0.zip |
| macOS binaries: | r-release (arm64): Mega2R_1.1.0.tgz, r-oldrel (arm64): Mega2R_1.1.0.tgz, r-release (x86_64): Mega2R_1.1.0.tgz, r-oldrel (x86_64): Mega2R_1.1.0.tgz |
| Old sources: | Mega2R archive |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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