Description Usage Arguments Details Value Author(s) See Also Examples

The function takes as inputs two adjacency matrices. Let X denote the observed number of edges in common between the two adjacency matrices. To test the significance of the correlation between the two data sources, the function performs N random edge permutations and random node permutations respectively. For each permutation test, the function outputs the proportion of N realizations that resulted in X edges or more at the intersection of the two datasources

1 | ```
getpvalue(act.mat, nonact.mat, num.iterations = 1000)
``` |

`act.mat` |
Adjacency matrix corresponding to first data source. That is, the i,j element of this matrix is 1 if data source one specifies a functional link between genes i and j |

`nonact.mat` |
Adjacency matrix corresponding to first data source. That is, the i,j element of this matrix is 1 if data source two specifies a functional link between genes i and j |

`num.iterations` |
Number of realizations from random edge (node) permutation to be obtained |

We note that the first adjacency matrix, denoted act.mat is the data source that is permutated with respect to edges or notes

A vector of length 2, where the first element is the P value from Random Edge Permutation and the second element is the P value from Random Node Permutation

Raji Balasubramanian rbalasub@hsph.harvard.edu

`permEdgesM2M`

, `permNodesM2M`

, `makeClustM`

1 2 3 4 5 6 7 8 |

```
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
[1] 0.58 0.68
```

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