compareProfilesLists: Compares two of expanded profiles

Description

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)

Usage

compareProfilesLists(expanded1, expanded2, common.expanded=NULL, relationType,
method = "lcombChisq", ab.approx = "asymptotic", confidence = 0.95, ...)

Arguments

expanded1

First expanded profile to be compared

expanded2

Second expanded profile to to be compared

common.expanded

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

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

#[NOT RUN] 
#data(ProstateIds)
#expandedWelsh <- expandedProfile(welsh01EntrezIDs[1:100], onto="MF",
#                        level=2, orgPackage="org.Hs.eg.db")
#expandedSingh <- expandedProfile(singh01EntrezIDs[1:100], onto="MF",
#                        level=2, orgPackage="org.Hs.eg.db")
#commonGenes <- intersect(welsh01EntrezIDs[1:100], singh01EntrezIDs[1:100])
#commonExpanded <- expandedProfile(commonGenes, onto="MF", level=2, orgPackage="org.Hs.eg.db")
#comparedMF<- compareProfilesLists (expandedWelsh, expandedSingh, commonExpanded, relationType="COMMON")
#print(comparedMF)
#print(compSummary(comparedMF))