compareProfilesLists {goProfiles} | R Documentation |
This function compares two lists (``sensu R lists'') of expanded profiles by successive calls to function texttt{compareGOProfiles} following the methodology developed by Sanchez, Salicru and Ocan~a (2007)
compareProfilesLists(expanded1, expanded2, common.expanded=NULL, relationType, method = "lcombChisq", ab.approx = "asymptotic", confidence = 0.95, ...)
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' |
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
Alex Sanchez
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
compareGeneLists
, expandedProfile
require(goProfiles) data(sampleProfiles) comparedMF<- compareProfilesLists (expandedWelsh01, expandedSingh01, relationType="DISJOINT") print(comparedMF) print(compSummary(comparedMF))