compareGeneLists: Compares two lists of genes by building (expanded) profiles and comparing them

Description

This function wraps all the needed steps to compare two lists of genes following the methodology developed by Sanchez, Salicru and Ocan\~a (2007)

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'

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

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

Examples

Run this code

data(prostateIds)
prostateCompared<- compareGeneLists (welsh01EntrezIDs[1:500],
singh01EntrezIDs[1:500], level=2, onto='MF', orgPackage="org.Hs.eg.db")
print(prostateCompared)
# print(compSummary(prostateCompared))