goProfiles (version 1.34.0)

expandedProfile: Builds expanded profiles

Description

Expanded profiles are used mainly for comparison of profiles based on the theory developed by Sanchez et al (2007) (see references)

Usage

expandedProfile(genelist, idType = "Entrez", onto = "ANY", level = 2,orgPackage=NULL, anotPackage=NULL, 
	multilevels = NULL, ord = TRUE, na.rm = TRUE, percentage = TRUE)

Arguments

genelist

List of genes on which the Profile has to be based

idType

Type of identifiers for the genes. Use 'Entrez' preferably

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'). This field must be provided if the gene list passed to the function is either a character vector of 'Entrez' (NCBI) identifiers or a character vector of probe names

anotPackage

Name of Bioconductor annotations package. This field must be provided if the gene list passed to the function is a character vector of probe names

ord

Set to 'TRUE' if the profile has to appear ordered by the category names

multilevels

If it is not NULL it must be a vector of GO categories that defines the level at where the profile is built

na.rm

Set to 'TRUE' if NAs should be removed

percentage

Set to 'TRUE' if the profile must be built using percentages

Value

An object of class GOProfile containing an expanded profile

Details

The function admits three types of entries: Entrez ('Entrez'), Bioconductor probe set names ('BioCprobes') or a special type of data frames ('GOTermsFrames'). If the identifier type are 'BioCprobes' then an annotation package name must be provided too.

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, Volume 137, Issue 12, Pages 3975-3989, 2007.

See Also

basicProfile

Examples

data(CD4Ids)
CD4.Expanded <-expandedProfile(genelist=CD4LLids[1:50], onto='MF', level=2, orgPackage="org.Hs.eg.db")