compareProfilesLists: Compares two of expanded profiles

In goProfiles: goProfiles: an R package for the statistical analysis of functional 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

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

See Also

compareGeneLists, expandedProfile

Examples

#[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))

goProfiles documentation built on Nov. 8, 2020, 8:12 p.m.