# pathway.mean.test

From topologyGSA v1.4.5
by Gabriele Sales

##### Testing the means of a pathway.

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

##### Usage

`pathway.mean.test(y1,y2,dag,alpha,perm.num=10000,variance=TRUE,paired=FALSE)`

##### Arguments

- 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
`gRbase`

for more details. - alpha
- significance level of the test.
- variance
- logical flag. If
`TRUE`

estimated variances s1 and s2 are reported. - perm.num
- number of permutations of the test.
- paired
- logical flag. If
`TRUE`

Hotelling test for paired samples is calculated and the test on the variances is not performed.

##### Details

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.

##### Value

- 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
`TRUE`

, this is not returned. - lambda.value
- the observed value of the test statistic for the
variance. If paired is
`TRUE`

, this is not returned. - qchisq.value
- the 1 - alpha quantile value of the null
distribution of the test statistic on the variance. If paired is
`TRUE`

, this is not returned. - cli.moral
- a list containing the cliques of the moral graph.
- var.equal
- logical flag. If
`TRUE`

variances are heteroschedastic. If paired is`TRUE`

, this is not returned. - 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
`TRUE`

, this is not returned. - df.mean
- the degrees of freedom of the null distribution for the
mean test. If paired is
`TRUE`

, this is not returned. - t.value
- the observed value of the test statistic for the mean.

##### References

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

##### See Also

##### Examples

```
data(examples)
pathway.mean.test(y1, y2, dag_bcell, 0.05, 100)
```

*Documentation reproduced from package topologyGSA, version 1.4.5, License: GPL-3*

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