plot.netgwas

A vector containing number of variables/markers in each group/chromosome. For example, the CviCol dataset that is provided in the package contains 5 chromosomes/ groups which the total number of markers is \(p = 90\), where the first 24 markers belong into chromosome 1, the next 14 markers into chromosome 2, ..., and chromosome 5 contains 19 markers. Thus, n.mrkr = c(24,14,17,16,19). If <code>n.mrkr = NULL</code>, in the graph visualization all markers are represented same colour.

n.markers

System reserved (No specific usage)

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Plot the graph path which is the output of two functions <code><a rd-options="" href="/link/netsnp?package=netgwas&version=0.0.1-1" data-mini-rdoc="netgwas::netsnp">netsnp</a></code>, <code><a rd-options="" href="/link/netphenogeno?package=netgwas&version=0.0.1-1" data-mini-rdoc="netgwas::netphenogeno">netphenogeno</a></code>.

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> .

Pariya Behrouzi

netgwas

Network-Based Genome Wide Association Studies

plot.netgwas function

Plot the graph path which is the output of two functions <code><a rd-options='' href='netsnp'>netsnp</a></code>, <code><a rd-options='' href='netphenogeno'>netphenogeno</a></code>.

plot.netgwas: plot for S3 class "netgwas"

Description

Usage

Arguments

References

See Also