R: Network-Based Genome Wide Association Studies

# Network-Based Genome Wide Association Studies

## Documentation for package ‘netgwas’ version 1.14.5

- DESCRIPTION file.

## Help Pages

netgwas-package | Network Based Genome Wide Association Studies
buildMap | linkage group detection and ordering markers for class "netgwasmap"
cal.pos | Estimate genetic map distances
cross2netgwas | 'cross' object to 'netgwas' data frame
cutoffs | Cut-points
CviCol | Arabidopsis thaliana genotype data
detect.err | Identiying likely genotyping error
lower.upper | Calculates lower band and upper band
netgwas2cross | netgwasmap object to cross object
netmap | Constructing linkage map for diploids and polyploids
netphenogeno | Reconstructs conditional dependence network among genetic loci and phenotypes
netsnp | Reconstructs intra- and inter- chromosomal conditional interactions among genetic loci
plot.netgwas | plot for S3 class "netgwas"
plot.netgwasmap | plot for S3 class "netgwasmap"
plot.select | Plot function for S3 class "select"
plot.simgeno | Plot function for 'S3' class '"simgeno"'
print.netgwas | Print function for S3 class "netgwas"
print.netgwasmap | Print function for S3 class "netgwasmap"
print.select | Print function for S3 class "select"
print.simgeno | Print function for S3 class "simgeno"
R.approx | The expectation of covariance using approximation method
R.gibbs | The expectation of covariance matrix using Gibbs sampling
selectnet | Model selection
simgeno | Generate genotype data based on Gaussian copula
simRIL | Generate genotype data of RIL
tetraPotato | tetraploid potato genotype data
thaliana | Arabidopsis thaliana phenotype and genotype data