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

Test the equality of the means in two experimental conditions for all the cliques of a pathway, conditioning on the results of the test on the concentration matrices

1 | ```
clique.mean.test(y1,y2,dag,alpha,perm.num=1000,paired=FALSE)
``` |

`y1` |
a matrix with n1 individuals (rows) in the first experimental condition and p genes (columns). |

`y2` |
a matrix with n2 individuals (rows) in the second experimental condition and p genes (columns). The genes in the two experimental conditions must be the same. |

`dag` |
graphNEL object, a directed acyclic graph (DAG) corresponding to the pathway of interest. See package |

`alpha` |
significance level of the test. |

`perm.num` |
number of permutation used by the test. |

`paired` |
logical flag. If |

The function tests the equality of the means of each clique of a
pathway in two experimental conditions, conditioning on the results of
`clique.var.test`

.
The graph of a pathway is first converted into a DAG, then the moral
graph is obtained and if the latter graph is decomposable then the
test is performed on all its cliques. If the moral graph is not
decomposable, its triangulated version is obtained and then the test
is performed on all its cliques.

The expression data may contain some genes differing from those in the pathway: in such case the function automatically takes the intersection between the two gene sets.

This function requires `gRBase`

and `qpgraph`

packages.

`p.value` |
p-value of the test on the mean for each clique. |

`p.value.var` |
p-value of the test on the variance for each clique. If paired is |

`cliques` |
the list of the corresponding cliques. |

`var.equal` |
logical, a vector with a TRUE for a significant clique and a FALSE otherwise. If paired is |

`t.value` |
the observed values of the statistic to test the mean for each clique. |

`lambda.value` |
the observed values of the statistic to test the
variance for each clique. If paired is |

`graph` |
the triangularized and moralized graph. |

M. Sofia Massa, Gabriele Sales

Massa, M.S., Chiogna, M., Romualdi, C. (2010). Gene set analysis exploiting the topology of a pathway. BMC Systems Biology, 4:121 http://www.biomedcentral.com/1752-0509/4/121

`pathway.var.test`

,`pathway.mean.test`

,
`clique.var.test`

,

1 2 3 | ```
data(examples)
clique.mean.test(y1, y2, dag_bcell, 0.05)
``` |

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