Package: Mega2R
Version: 1.0.9
Date: 2021-12-04
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: 7.1.0
VignetteBuilder: knitr
Packaged: 2021-12-04 16:32:14 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: 2021-12-06 18:10:06 UTC