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>.
