Network-Based Genome Wide Association Studies

Documentation for package ‘netgwas’ version 1.14.3

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