Usage
compareGeneLists(genelist1, genelist2, idType = "Entrez", onto = "ANY",
level = 2, orgPackage,
method = "lcombChisq", ab.approx = "asymptotic", confidence = 0.95, compareFunction="compareGOProfiles", ...)
Arguments
genelist1
First gene set to be compared
genelist2
Second gene set to be compared
idType
Type of identifiers for the genes. May be 'Entrez' (default), BiocProbes or GoTermsFrame. See the 'Details' section below
onto
Ontology on which the profile has to be built
level
Level of the ontology at which the profile has to be
built
orgPackage
Name of a Bioconductor's organism annotations package
('org.Xx-eg-db')
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)
compareFunction
Allows to use 'fitGOProfile' (sample vs population) or 'compareGOProfiles' (sample1 vs sample2)
...
Other arguments for the methods 'basicProfile' or 'compareGoProfiles'