Network-Based Genome Wide Association Studies
linkage group detection and ordering markers for class "netgwasmap"
Estimate genetic map distances
cross object to netgwas data frame
Cut-points
Identiying likely genotyping error
Calculates lower band and upper band
netgwas-internal
Network Based Genome Wide Association Studies
netgwasmap object to cross object
Constructing linkage map for diploids and polyploids
Reconstructs conditional dependence network among genetic loci and phe...
Reconstructs intra- and inter- chromosomal conditional interactions am...
plot for S3 class "netgwas"
plot for S3 class "netgwasmap"
Plot function for S3 class "select"
Plot function for S3 class "simgeno"
Print function for S3 class "netgwas"
Print function for S3 class "netgwasmap"
Print function for S3 class "select"
Print function for S3 class "simgeno"
The expectation of covariance using approximation method
The expectation of covariance matrix using Gibbs sampling
Model selection
Generate genotype data based on Gaussian copula
Generate genotype data of RIL
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>.