# getpvalue: Function to obtain P values from the Edge permutation and... In GraphAT: Graph Theoretic Association Tests

## Description

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

## Usage

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

## Arguments

 `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

## Details

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

## Value

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

## Author(s)

Raji Balasubramanian rbalasub@hsph.harvard.edu

`permEdgesM2M`, `permNodesM2M`, `makeClustM`

## Examples

 ```1 2 3 4 5 6 7 8``` ```act.mat <- matrix(0,3,3) act.mat[2,1] <- 1 act.mat[3,1] <- 1 nonact.mat <- matrix(0,3,3) nonact.mat[2,1] <- 1 nonact.mat[3,2] <- 1 p.val <- getpvalue(act.mat, nonact.mat, num.iterations = 100) print(p.val) ```

### Example output

```Loading required package: graph

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':

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

 0.58 0.68
```

GraphAT documentation built on Nov. 8, 2020, 5:01 p.m.