topologyGSA (version 1.4.5)

pathway.mean.test: Testing the means of a pathway.

Description

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.

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.

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.

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

pathway.var.test, clique.var.test, clique.mean.test,

Examples

data(examples)

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