CRAN/E | Mega2R

Mega2R

Accessing and Processing a 'Mega2' Genetic Database

Installation

About

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 ). 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.

watson.hgen.pitt.edu/mega2/mega2r/
Bug report File report

Key Metrics

Version 1.1.0
R ≥ 3.5.0
Published 2023-12-21 213 days ago
Needs compilation? yes
License GPL-2
CRAN checks Mega2R results

Downloads

Yesterday 4 +33%
Last 7 days 72 +22%
Last 30 days 278 -8%
Last 90 days 864 -23%
Last 365 days 3.563 +15%

Maintainer

Maintainer

Daniel E. Weeks

Authors

Robert V. Baron

aut

Daniel E. Weeks

aut / cre

University of Pittsburgh

cph

Material

NEWS
Reference manual
Package source

Vignettes

Mega2R Tutorial

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

Mega2R archive

Depends

R ≥ 3.5.0
SKAT
pedgene
gdsfmt

Imports

AnnotationDbi
DBI
GenomeInfoDb
RSQLite
methods
famSKATRC
kinship2

Suggests

knitr
rmarkdown
formatR
TxDb.Hsapiens.UCSC.hg19.knownGene
org.Hs.eg.db

LinkingTo

Rcpp