sig.net: Significant Network

Description Usage Arguments Examples

View source: R/netpredictor.R

Description

Significance of Bipartite networks

Usage

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sig.net(data, g, Amatrix, num.permutation = 10, adjp.cutoff = 0.05,
  p.adjust.method = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY",
  "fdr"), parallel = TRUE, multicores = NULL, verbose = T)

Arguments

data

n x m Adjancency matrix of seeds or dataframe of pairs.

g

igrah object of bipartite indcident adjacency matrix.

Amatrix

Affinity matrix computed from biNetWalk or uNetWalk.

num.permutation

number of permutation of Affinity matrix needed to performed.

adjp.cutoff

pvalue cutoff 0.05

p.adjust.method

Adjusting the pvalue by diiferent method.It uses method from the stats package.

parallel

Using parallization either True or False

multicores

If parallisation is set TRUE number of cores to perform parallel computaion.

verbose

For verbose output.

Examples

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data(Enzyme)
A <- enzyme_ADJ
S1 = enzyme_Gsim
S2 = enzyme_Csim
g1 = graph.incidence(A)
Q = biNetwalk(g1,s1=S1,s2=S2,normalise="laplace", dataSeed=NULL, file=NULL,restart=0.8,verbose=T)
Z = sig.net(data=A,g=g1,Amatrix=Q,num.permutation=100,adjp.cutoff=0.01,p.adjust.method="BH",parallel=FALSE,verbose=T)

abhik1368/netpredictor documentation built on May 10, 2017, 9:09 p.m.