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

To calculate p-value for the null hypothesis that there is no gene-gene interaction. For gene expression data with M genes, a p-value matrix under MxM single null hypotheses (each two genes have no interaction) is computed; besides, matrices with correct p-values are output: corrected permutation method using a distribution of MxMxP (P number of permutations) null hypotheses tests (multi.perm.p.value). p-values are calculated based on the adjacency matrix for gene-gene interaction computed by function *gene.similarity*.

1 | ```
gene.pvalue(EXP, measure, net.trim, n.replica = 400)
``` |

`EXP` |
Gene expression data in form of a matrix. Row stands for genes and column for experiments. |

`measure` |
Metric used to calculate similarity between genes: "corr" for correlation, "MI" for mutual information. |

`net.trim` |
Method used to trim the network: "mrnet", "clr", "aracne" and "none" . "mrnet" infers a network using the maximum relevance/minimum redundancy feature selection method; "clr" use the CLR algorithm; "aracne" applies the data processing inequality to all triplets of nodes in order to remove the least significant edge in each triplet. These options come from the package |

`n.replica` |
Number of permutations used for the correction of multiple hypothesis testing; default value is 400. |

Normally, in a permutation method, we use the empirical distribution of some statistics to estimate the p-value. To get a simple p-value for no interaction between gene i and j, empirical distribution of a vector with length of P (number of replicates) is used; to correct for multiple hypothesis with permutations, an empirical distribution of a vector with length of PxM (M being the number of hypotheses tested) is used.

`single.perm.p.value` |
A matrix of single p-values obtained with permutation method + beta distribution for extreme values (for MI) or obtained with the exact distribution computed directly by |

`multi.perm.p.value` |
A matrix of corrected p-values obtained with permutation method |

Yin Jin, Hesen Peng, Lei Wang, Raffaele Fronza, Yuanhua Liu and Christine Nardini

1 2 3 4 |

BUS documentation built on Nov. 1, 2018, 4:28 a.m.

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