netgwas: Network-Based Genome Wide Association Studies

A multi-core R package that contains a set of tools based on copula graphical models for accomplishing the three interrelated goals in genetics and genomics in an unified way: (1) linkage map construction, (2) constructing linkage disequilibrium networks, and (3) exploring high-dimensional genotype-phenotype network and genotype- phenotype-environment interactions networks. The 'netgwas' package can deal with biparental inbreeding and outbreeding species with any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes), tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where number of variables p is considerably larger than number of sample sizes (p >> n). The computations is memory-optimized using the sparse matrix output. The 'netgwas' implements the methodological developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <doi:10.1093/bioinformatics/bty777>.

Version:	1.14.3
Depends:	R (≥ 3.1.0)
Imports:	Matrix (≥ 1.4-1), igraph, qtl, parallel, methods, glasso, MASS, huge, tmvtnorm
Suggests:	testthat
Published:	2024-03-19
DOI:	10.32614/CRAN.package.netgwas
Author:	Pariya Behrouzi [aut, cre], Ernst C. Wit [ctb]
Maintainer:	Pariya Behrouzi <pariya.behrouzi at gmail.com>
License:	GPL-3
NeedsCompilation:	no
Citation:	netgwas citation info
CRAN checks:	netgwas results

Documentation:

Reference manual:

netgwas.pdf

Downloads:

Package source:	netgwas_1.14.3.tar.gz
Windows binaries:	r-devel: netgwas_1.14.3.zip, r-release: netgwas_1.14.3.zip, r-oldrel: netgwas_1.14.3.zip
macOS binaries:	r-release (arm64): netgwas_1.14.3.tgz, r-oldrel (arm64): netgwas_1.14.3.tgz, r-release (x86_64): netgwas_1.14.3.tgz, r-oldrel (x86_64): netgwas_1.14.3.tgz
Old sources:	netgwas archive

Reverse dependencies:

Reverse imports:

netShiny

Linking:

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