create.network: Constructs the SNV-SNV network

In lgl15/cnmtf: Prioritisation of single nucleotide variants using Corrected non-negative matrix tri-factorisation

Description

Function to create a SNV-SNV network using a PPI reference network

Usage

create.network(net.type = "ppi", dedges = NULL, remove.highLD = TRUE,
  ld.tao = 0.8, res.ld = NULL, keep.with.LD = NULL, R.snps = NULL,
  work.dat = NULL, trait.project = NULL, n.cores = 4, tmap = NULL,
  plot.file = NULL, venn.diag = FALSE, snps.known = NULL)

Arguments

net.type	Type of reference network. Default "ppi"
dedges	Object with edges from reference network
remove.highLD	Expand SNV consequences to SNVs in high LD
ld.tao	Treshold of LD. Default 0.8
res.ld	Table of LD
keep.with.LD	List of SNPs to include even if they are in LD
R.snps	List of SNVs in R
work.dat	Working directory
trait.project	Trait
n.cores	Number of cores for parallel computing
tmap	Mapping of SNPs to genes
plot.file	File to print Venn diagrams and node degree distribution
venn.diag	Logical. Print Venn diagrams. Default = FALSE.
snps.known	SNVs known to be associated with the trait

Value

• Wu, G: adjacency matrix and graph object of the network

• Table with node properties to be used in Cytoscape

• Venn diagrams of damaging variants and node degree distribution

Author(s)

Luis G. Leal, [e-mail]

See Also

Other Preprocessing functions: coding.scheme, construct.Vo, construct.Wu, degree.distribution, kernels.cnmtf, mapply.snpt.synthetic.gwas, rownet.hub, snpt.synthetic.gwas

lgl15/cnmtf documentation built on May 28, 2019, 6:33 p.m.