clique.var.test: Testing the concentration matrices of all cliques of a pathway.

Description

Test the equality of concentration matrices in two experimental conditions for all cliques of a pathway

Usage

clique.var.test(y1,y2,dag,alpha)

Arguments

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

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.

Value

p.value: the observed value of the significance level.
cliques: the list of cliques where the test is performed.
var.equal: logical, a vector with a TRUE for a significant clique and a FALSE otherwise.
lambda.var: the observed value of the statistic.
graph: the triangulated and moral graphs.

Details

The function tests the equality of the concentration matrices of each clique of a pathway in two experimental conditions. 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.

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

Examples

Run this code

data(examples)

clique.var.test(y1, y2, dag_bcell, 0.05)

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