conversionFunctions {goProfiles} | R Documentation |
These functions transform data from one classtype into another, or pack simple processes such as compute the profiles needed for one annotations package.
as.GOTerms.frame(myGOTermsList, na.rm=TRUE) as.GOTerms.list(genelist, probeType, orgPackage=NULL, anotPkg=NULL, onto="any", na.rm=FALSE) BioCpack2EntrezIDS(anotPkg, na.rm=FALSE) BioCpack2Profiles(anotPkg, orgPackage, level=2, na.rm=FALSE, expanded=FALSE) BioCprobes2Entrez(probeslist , anotPkg, na.rm=TRUE) GOTermsFrame2GOTermsList(myGOTermsFrame, evid=FALSE)
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 |
Not yet available
Every function returns a transformed object or a list of computed profiles
Alex Sanchez
data(CD4Ids) myGOTermsList <- GOTermsList(CD4LLids[1:5], orgPkg="org.Hs.eg.db") myGOTermsFrame<- as.GOTerms.frame(myGOTermsList, na.rm=TRUE) GOTermsFrame2GOTermsList(myGOTermsFrame, evid=FALSE)