This function compares two lists (“sensu R lists”) of expanded profiles by successive
calls to function compareGOProfiles following
the methodology developed by Sanchez, Salicru and Ocan~a (2007)
Expanded profile made from the genes appearing in both lists of genes
relationType
Type of relation between gene lists compared through the expanded profiles. It can be INCLUSION, INTERSECTION or DISJOINT
method
The approximation method to the sampling distribution under the null hypothesis specifying that the samples pn and qm come from the same population. See the 'Details' section below
confidence
The confidence level of the confidence interval in the result
ab.approx
The approximation used for computing 'a' and 'b' coefficients (see details)
...
Other arguments for the methods 'basicProfile' or 'compareGoProfiles'
Value
The result of the comparison is a list with a variable number of arguments, depending for which ontologies has been performed the comparison. Each list member is an object of class 'htest' corresponding to the output of the function compareGOProfiles
Author(s)
Alex Sanchez
References
Sanchez-Pla, A., Salicru, M. and Ocana, J.
Statistical methods for the analysis of high-throughput data based on
functional profiles derived from the gene ontology.
Journal of Statistical Planning and Inference, 2007