Package: Mega2R
Version: 1.0.2
Date: 2018-04-03
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 output the
     'Mega2R' data as a VCF file and related files (for phenotype and
     family data), and to convert the data frames into 'GenABEL'
     gwaa.data-class objects.  
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 (>= 3.3), GenABEL, SKAT, pedgene,
License: GPL-2
LinkingTo: Rcpp
Imports: AnnotationDbi, DBI, GenomeInfoDb, RSQLite, methods
Suggests: knitr, rmarkdown, formatR, TxDb.Hsapiens.UCSC.hg19.knownGene,
        org.Hs.eg.db
NeedsCompilation: yes
RoxygenNote: 6.0.1
LazyData: true
VignetteBuilder: knitr
Packaged: 2018-04-03 17:13:47 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: 2018-04-03 17:51:39 UTC
Built: R 3.3.3; x86_64-w64-mingw32; 2018-04-22 16:58:35 UTC; windows
Archs: i386, x64
