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Mega2R
View on CRAN: Click
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Download and install Mega2R package within the R console
Install from CRAN:
install.packages("Mega2R")
Install from Github:
library("remotes")
install_github("cran/Mega2R")
Install by package version:
library("remotes")
install_version("Mega2R", "1.1.0")
Attach the package and use:
library("Mega2R")
Maintained by
Daniel E. Weeks
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-11-02
Latest Update: 2021-12-06
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
). 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.
How to cite:
Daniel E. Weeks (2017). Mega2R: Accessing and Processing a 'Mega2' Genetic Database. R package version 1.1.0, https://cran.r-project.org/web/packages/Mega2R. Accessed 21 Nov. 2024.
Previous versions and publish date:
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Other R packages that Mega2R depends,
imports, suggests or enhances
Complete documentation for Mega2R
Functions, R codes and Examples using
the Mega2R R package
Some associated functions: DOSKAT . DOfamSKATRC . DOpedgene . Mega2ENVGenABEL . Mega2GenABEL . Mega2GenABELClean . Mega2GenABELtst . Mega2R-TBLS . Mega2R-TBLSFilter . Mega2R . Mega2RVersion . Mega2SKAT . Mega2VCF . Mega2famSKATRC . Mega2gdsfmt . Mega2pedgene . applyFnToGenes . applyFnToMarkers . applyFnToRanges . clean_mega2rtutorial_data . computeDosage . dbmega2_import . dmpPed . dump_mega2rtutorial_data . getAlleles . getgenotype_person . getgenotypes . getgenotypes_R . getgenotypesdos . getgenotypesgenabel . getgenotypesraw . init_SKAT . init_famSKATRC . init_pedgene . mkAlleles . mkGenABELcoding . mkGenABELgenotype . mkGenABELphenotype . mkGenABELtfam . mkGenABELtped . mkMarkers . mkVCFfam . mkVCFfreq . mkVCFhdr . mkVCFmap . mkVCFpen . mkVCFphe . mk_markers_with_skip . mk_unified_genotype_table . mkfam . mkphenotype . read.Mega2DB . resetMega2ENV . setAnnotations . setRanges . setfam . showMapNames . showMega2ENV . showPhenoNames . uniqueFamMember . where_mega2rtutorial_data .
Some associated R codes: RcppExports.R . mega2famskatrc.R . mega2gdsfmt.R . mega2genabel.R . mega2genabelexternal.R . mega2genabeltst.R . mega2pedgene.R . mega2rcreate.R . mega2riterate.R . mega2rtutorial.R . mega2skat.R . mega2vcf.R . zzz.R . Full Mega2R package functions and examples
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