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

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

1 | ```
pathway.mean.test(y1,y2,dag,alpha,perm.num=10000,variance=TRUE,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. |

`variance` |
logical flag. If |

`perm.num` |
number of permutations of the test. |

`paired` |
logical flag. If |

The function tests the equality of the means of two
experimental conditions, conditioning on the result of
`pathway.var.test`

.

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` |
the p-value of the test on the mean. |

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

`lambda.value` |
the observed value of the test statistic for the
variance. If paired is |

`qchisq.value` |
the 1 - alpha quantile value of the null
distribution of the test statistic on the variance. If paired is |

`cli.moral` |
a list containing the cliques of the moral graph. |

`var.equal` |
logical flag. If |

`graph` |
a graphNEL object representing the moral graph. |

`df.var` |
the degrees of freedom of the null distribution for the
variance test. If paired is |

`df.mean` |
the degrees of freedom of the null distribution for the
mean test. If paired is |

`t.value` |
the observed value of the test statistic for the mean. |

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`

, `clique.var.test`

,
`clique.mean.test`

,

1 2 3 | ```
data(examples)
pathway.mean.test(y1, y2, dag_bcell, 0.05, 100)
``` |

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