Test the equality of means in two experimental conditions for a pathway, conditioning on the result of the test on the concentration matrices
pathway.mean.test(y1,y2,dag,alpha,perm.num=10000,variance=TRUE,paired=FALSE)
the p-value of the test on the mean.
the p-value of the test on the variance. If paired is TRUE
, this is not returned.
the observed value of the test statistic for the
variance. If paired is TRUE
, this is not returned.
the 1 - alpha quantile value of the null
distribution of the test statistic on the variance. If paired is TRUE
, this is not returned.
a list containing the cliques of the moral graph.
logical flag. If TRUE
variances are heteroschedastic. If paired is TRUE
, this is not returned.
a graphNEL object representing the moral graph.
the degrees of freedom of the null distribution for the
variance test. If paired is TRUE
, this is not returned.
the degrees of freedom of the null distribution for the
mean test. If paired is TRUE
, this is not returned.
the observed value of the test statistic for the mean.
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.
graphNEL object, a directed acyclic graph (DAG) corresponding to the pathway of interest. See package gRbase
for more details.
significance level of the test.
logical flag. If TRUE
estimated variances s1 and s2 are reported.
number of permutations of the test.
logical flag. If TRUE
Hotelling test for paired samples is calculated and the test on the variances is not performed.
M. Sofia Massa, Gabriele Sales
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.
Massa, M.S., Chiogna, M., Romualdi, C. (2010). Gene set analysis exploiting the topology of a pathway. BMC Systems Biology, 4:121 https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-121
pathway.var.test
, clique.var.test
,
clique.mean.test
,
data(examples)
pathway.mean.test(y1, y2, dag_bcell, 0.05, 100)
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