Package: Mega2R
Version: 1.1.0
Date: 2023-12-21
Title: 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
     <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.
Authors@R: c(person(c("Robert","V."), "Baron", email = "rvb5@pitt.edu",  role = c("aut")),
             person(c("Daniel","E."), "Weeks",    email = "weeks@pitt.edu", role = c("aut","cre")),
             person("","University of Pittsburgh",role=c("cph")))
URL: https://watson.hgen.pitt.edu/mega2/mega2r/
BugReports: https://groups.google.com/forum/#!forum/mega2-users
Depends: R (>= 3.5.0), SKAT, pedgene, gdsfmt
License: GPL-2
LinkingTo: Rcpp
biocViews: Genetics
Imports: AnnotationDbi, DBI, GenomeInfoDb, RSQLite, methods, famSKATRC,
        kinship2
Suggests: knitr, rmarkdown, formatR, TxDb.Hsapiens.UCSC.hg19.knownGene,
        org.Hs.eg.db
NeedsCompilation: yes
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Packaged: 2023-12-21 21:47:27 UTC; dweeks
Author: Robert V. Baron [aut],
  Daniel E. Weeks [aut, cre],
  University of Pittsburgh [cph]
Maintainer: Daniel E. Weeks <weeks@pitt.edu>
Repository: CRAN
Date/Publication: 2023-12-21 22:40:10 UTC
Built: R 4.3.0; x86_64-apple-darwin20; 2023-12-22 00:03:34 UTC; unix
Archs: Mega2R.so.dSYM
