netgwas v0.0.1-1

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Network-Based Genome Wide Association Studies

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) network, and (3) exploring high-dimensional genotype-phenotype network and genotype-phenotype-environment interactions network. For this purpose, we use conditional (in)dependence 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) <arXiv:1710.00894> and Behrouzi and Wit (2017) <arXiv:1710.01063> .

Functions in netgwas

Name Description
cutoffs Cut-points
CviCol Arabidopsis thaliana genotype data
buildMap linkage group detection and ordering markers for class "netgwasmap"
R.approx The expectation of covariance using approximation method
netgwas-internal netgwas-internal
netphenogeno Reconstructs conditional dependence network among genetic loci and phenotypes
netgwas-package Network Based Genome Wide Association Studies
lower.upper Calculates lower band and upper band
netmap Constructing linkage map for diploids and polyploids
R.gibbs The expectation of covariance matrix using Gibbs sampling
netsnp Reconstructs intra- and inter- chromosomal conditional interactions among genetic loci
plot.netgwasmap plot for S3 class "netgwasmap"
plot.netgwas plot for S3 class "netgwas"
plot.select Plot function for S3 class "select"
print.netgwasmap Print function for S3 class "netgwasmap"
print.select Print function for S3 class "select"
plot.simgeno Plot function for S3 class "simgeno"
print.simgeno Print function for S3 class "simgeno"
print.netgwas Print function for S3 class "netgwas"
selectnet Model selection
thaliana Arabidopsis thaliana phenotype and genotype data
simgeno Generate genotype data based on Gaussian copula
tetraPotato tetraploid potato genotype data
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Details

Type Package
License GPL-3
Date 2017-11-24
NeedsCompilation no
Packaged 2017-12-01 12:56:17 UTC; Pariya
Repository CRAN
Date/Publication 2017-12-01 18:20:24 UTC

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