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

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 [e-mail]

See Also

permEdgesM2M, permNodesM2M, makeClustM

Examples

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
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

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