Package: netgwas
Type: Package
Title: Network-Based Genome Wide Association Studies
Version: 1.10
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Depends: R (>= 3.1.0)
Imports: Matrix, igraph, qtl, parallel, methods, glasso, MASS, RBGL,
huge,tmvtnorm
Suggests: testthat
Description: A multi-core R package that contains a set of tools based on undirected graphical
models for accomplishing three important and interrelated goals in genetics: (1)
linkage map construction, (2) reconstructing intra- and inter-chromosomal conditional
interactions (linkage disequilibrium) networks, and (3) exploring high-dimensional
genotype-phenotype network and genotype-phenotype-environment interactions network.
We use conditional independence relationships between variables.
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 larger than number of sample sizes (p >> n). The computations
is memory-optimized using the sparse matrix output. The package is implemented the recent
developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287> and Behrouzi and Wit (2017)
<arXiv:1710.01063>.
NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
License: GPL-3
Date: 2019-04-12
NeedsCompilation: no
Packaged: 2019-04-12 13:36:47 UTC; behro001
Repository: CRAN
Date/Publication: 2019-04-12 14:02:43 UTC

Package: netgwas
Type: Package
Title: Network-Based Genome Wide Association Studies
Version: 1.11
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Depends: R (>= 3.1.0)
Imports: Matrix, igraph, qtl, parallel, methods, glasso, MASS, RBGL,
huge,tmvtnorm
Suggests: testthat
Description: 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 package is
implemented the recent methodological developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287>
and Behrouzi and Wit (2017) <doi:10.1093/bioinformatics/bty777>.
NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
License: GPL-3
Date: 2019-10-14
NeedsCompilation: no
Packaged: 2019-10-15 09:03:50 UTC; behro001
Repository: CRAN
Date/Publication: 2019-10-15 15:00:02 UTC