compareGeneLists: Compares two lists of genes by building (expanded) profiles...

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

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

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

compareGOProfiles, basicProfile

Examples

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

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