goProfiles (version 1.34.0)

conversionFunctions: Functions to transformconvert objects between different types

Description

These functions transform data from one classtype into another, or pack simple processes such as compute the profiles needed for one annotations package.

Usage

as.GOTerms.frame(myGOTermsList, na.rm=TRUE)
as.GOTerms.list(genelist, probeType, orgPackage=NULL, anotPkg=NULL, onto="any", na.rm=TRUE)
BioCpack2EntrezIDS(anotPkg, na.rm=TRUE)
BioCpack2Profiles(anotPkg, orgPackage, level=2, na.rm=TRUE, expanded=FALSE)
BioCprobes2Entrez(probeslist , anotPkg, na.rm=TRUE)
GOTermsFrame2GOTermsList(myGOTermsFrame, evid=FALSE)

Arguments

myGOTermsList

GOTermsList object to transform

myGOTermsFrame

GOTermsFrame object to transform

genelist

List of genes (Entrez Ids) to transform

evid

Type of evidence supporting the selected GO Terms

na.rm

Flag indicating if those ids returning NA must be removed from the output

probeType

Type of probes to transform into Entrez Ids

probeslist

List of probes to transform into Entrez Ids

orgPackage

Name of the organism ('org.Xx.eg.db') annotation package

anotPkg

Name of the chip annotation package

level

GO level at which the profile is built

onto

ontology

expanded

Flag to decide if an expanded profile has to be computed

Value

Every function returns a transformed object or a list of computed profiles

Details

Not yet available

Examples

data(CD4Ids)
myGOTermsList <- GOTermsList(CD4LLids[1:5], orgPkg="org.Hs.eg.db")
myGOTermsFrame<- as.GOTerms.frame(myGOTermsList, na.rm=TRUE)
GOTermsFrame2GOTermsList(myGOTermsFrame, evid=FALSE)