edgeTest | R Documentation |

Nodes scores equality test between network

edgeBetweennessEdgeTest( expr, labels, adjacencyMatrix, numPermutations = 1000, options = NULL, BPPARAM = NULL )

`expr` |
Matrix of variables (columns) vs samples (rows) |

`labels` |
a vector in which a position indicates the phenotype of the corresponding sample or state |

`adjacencyMatrix` |
a function that returns the adjacency matrix for a given variables values matrix |

`numPermutations` |
number of permutations that will be carried out in the permutation test |

`options` |
argument non used in this function |

`BPPARAM` |
An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation, or a list of BiocParallelParam instances, to be applied in sequence for nested calls to BiocParallel functions. MulticoreParam() |

A table, containing on the columns, the following informations for each variable (rows): "Test Statistic" - difference among the degree centrality of a node in two or more networks associated with each phenotype "Nominal p-value" - the Nominal p-value of the test "Q-value" - the q-value of the test, correction of p-value by FDR to many tests "Factor n" - the node degree centrality in each network compared

set.seed(1) expr <- as.data.frame(matrix(rnorm(120),40,30)) labels<-data.frame(code=rep(0:3,10),names=rep(c("A","B","C","D"),10)) adjacencyMatrix1 <- adjacencyMatrix(method="spearman", association="pvalue", threshold="fdr", thr.value=0.05, weighted=FALSE) # The numPermutations number is 1 to do a faster example, but we advise to use unless 1000 permutations in real analysis # Edge betweenness centrality test diffNetAnalysis(method=edgeBetweennessEdgeTest, varFile=expr, labels=labels, varSets=NULL, adjacencyMatrix=adjacencyMatrix1, numPermutations=1, print=TRUE, resultsFile=NULL, seed=NULL, min.vert=5, option=NULL)

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