conversionFunctions {goProfiles}R Documentation

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=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)

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

Details

Not yet available

Value

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

Author(s)

Alex Sanchez

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)

[Package goProfiles version 1.4.0 Index]