basicProfile: Builds basic functional profile

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

Description

Compute basic functional profile for a given list of genes/GO identifiers, a given ontology at a given level of the GO

Usage

basicProfile(genelist, idType = "Entrez", onto = "ANY", level = 2, orgPackage=NULL, 
anotPackage=NULL, 	ord = TRUE, multilevels = NULL, 
empty.cats = TRUE, cat.names = TRUE, na.rm = TRUE)

Arguments

genelist	List of genes on which the Profile has to be based
idType	Type of identifiers for the genes. May be 'Entrez' (default), BiocProbes or GoTermsFrame (see details 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'). 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's microarray 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
empty.cats	Set to 'TRUE' if empty categories should appear in the profile
cat.names	Set to 'TRUE' if the profile has to contain the names of categories
na.rm	Set to 'TRUE' if NAs should be removed

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.

Value

An object of class GOProfile (one or more data frames in a list named by the ontologies)

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

See Also

expandedProfile

Examples

data(CD4Ids)
CD4.MF.Profiles <-basicProfile(genelist=CD4LLids, onto='MF', level=2, orgPackage="org.Hs.eg.db")
print(CD4.MF.Profiles)

alexsanchezpla/goProfiles documentation built on May 28, 2019, 4:54 p.m.