# dCommSignif: Function to test the significance of communities within a... In dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

## Description

`dCommSignif` is supposed to test the significance of communities within a graph. For a community of the graph, it first calculates two types of degrees for each node: degrees based on parters only within the community itself, and the degrees based on its parters NOT in the community but in the graph. Then, it performs two-sample Wilcoxon tests on these two types of degrees to produce the signficance level (p-value)

## Usage

 `1` ```dCommSignif(g, comm) ```

## Arguments

 `g` an object of class "igraph" or "graphNEL" `comm` an object of class "communities". Details on this class can be found at http://igraph.org/r/doc/communities.html

## Value

• `significance`: a vector of p-values (significance)

## Note

none

`dCommSignif`

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23``` ```# 1) generate an vector consisting of random values from beta distribution x <- rbeta(1000, shape1=0.5, shape2=1) # 2) fit a p-value distribution under beta-uniform mixture model fit <- dBUMfit(x, ntry=1, hist.bum=FALSE, contour.bum=FALSE) # 3) calculate the scores according to the fitted BUM and fdr=0.01 # using "pdf" method scores <- dBUMscore(fit, method="pdf", fdr=0.05, scatter.bum=FALSE) names(scores) <- as.character(1:length(scores)) # 4) generate a random graph according to the ER model g <- erdos.renyi.game(1000, 1/100) # 5) produce the induced subgraph only based on the nodes in query subg <- dNetInduce(g, V(g), knn=0) # 6) find the module with the maximum score module <- dNetFind(subg, scores) # 7) find the module and test its signficance comm <- walktrap.community(module, modularity=TRUE) significance <- dCommSignif(module, comm) ```

### Example output

```Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

decompose, spectrum

The following object is masked from 'package:base':

union