conversionFunctions: Functions to transformconvert objects between different types

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

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

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)

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