XGR (version 1.1.5)

xDefineOntology: Function to define ontology and its annotations

Description

xDefineOntology is supposed to define ontology and its annotations. It returns an object of class "aOnto".

Usage

xDefineOntology(ontology = c(NA, "GOBP", "GOMF", "GOCC", "PSG", "PS",
"PS2", "SF", "Pfam", "DO", "HPPA", "HPMI", "HPCM", "HPMA", "MP", "EF",
"MsigdbH", "MsigdbC1", "MsigdbC2CGP", "MsigdbC2CPall", "MsigdbC2CP",
"MsigdbC2KEGG", "MsigdbC2REACTOME", "MsigdbC2BIOCARTA", "MsigdbC3TFT",
"MsigdbC3MIR", "MsigdbC4CGN", "MsigdbC4CM", "MsigdbC5BP", "MsigdbC5MF",
"MsigdbC5CC", "MsigdbC6", "MsigdbC7", "DGIdb", "GTExV4", "GTExV6p",
"GTExV7", "CreedsDisease", "CreedsDiseaseUP", "CreedsDiseaseDN",
"CreedsDrug", "CreedsDrugUP", "CreedsDrugDN", "CreedsGene",
"CreedsGeneUP", "CreedsGeneDN", "KEGG", "KEGGmetabolism",
"KEGGgenetic",
"KEGGenvironmental", "KEGGcellular", "KEGGorganismal", "KEGGdisease",
"REACTOME", "REACTOME_ImmuneSystem", "REACTOME_SignalTransduction",
"CGL", "SIFTS2GOBP", "SIFTS2GOMF", "SIFTS2GOCC", "EnrichrARCHS4Cells",
"EnrichrARCHS4Tissues", "EnrichrHumanGeneAtlas",
"EnrichrTissueHumanProteomeMap", "EnrichrTissueProteomicsDB",
"EnrichrAchillesFitnessD", "EnrichrAchillesFitnessI", "EnrichrDSigDB",
"EnrichrOMIM", "EnrichrOMIMexpanded", "EnrichrdbGaP",
"EnrichrJensenDiseases", "EnrichrJensenTissues", "EnrichrBioCarta",
"EnrichrKEGG", "EnrichrNCIpathway", "EnrichrPanther",
"EnrichrReactome",
"EnrichrWikiPathways", "EnrichrhuMAP", "EnrichrChEA",
"EnrichrConsensusTFs", "EnrichrEncodeTF", "EnrichrTFlof",
"EnrichrTFpert"), ontology.customised = NULL,
anno.identity = c("GeneID", "Symbol"), verbose = T,
RData.location = "http://galahad.well.ox.ac.uk/bigdata")

Arguments

ontology

the ontology supported currently. It can be "GOBP" for Gene Ontology Biological Process, "GOMF" for Gene Ontology Molecular Function, "GOCC" for Gene Ontology Cellular Component, "PSG" for phylostratigraphy (phylostratific age), "PS" for sTOL-based phylostratific age information, "PS2" for the collapsed PS version (inferred ancestors being collapsed into one with the known taxonomy information), "SF" for SCOP domain superfamilies, "Pfam" for Pfam domain families, "DO" for Disease Ontology, "HPPA" for Human Phenotype Phenotypic Abnormality, "HPMI" for Human Phenotype Mode of Inheritance, "HPCM" for Human Phenotype Clinical Modifier, "HPMA" for Human Phenotype Mortality Aging, "MP" for Mammalian Phenotype, "EF" for Experimental Factor Ontology (used to annotate GWAS Catalog genes), Drug-Gene Interaction database ("DGIdb") for druggable categories, tissue-specific eQTL-containing genes from GTEx ("GTExV4", "GTExV6p" and "GTExV7"), crowd extracted expression of differential signatures from CREEDS ("CreedsDisease", "CreedsDiseaseUP", "CreedsDiseaseDN", "CreedsDrug", "CreedsDrugUP", "CreedsDrugDN", "CreedsGene", "CreedsGeneUP" and "CreedsGeneDN"), KEGG pathways (including 'KEGG' for all, 'KEGGmetabolism' for 'Metabolism' pathways, 'KEGGgenetic' for 'Genetic Information Processing' pathways, 'KEGGenvironmental' for 'Environmental Information Processing' pathways, 'KEGGcellular' for 'Cellular Processes' pathways, 'KEGGorganismal' for 'Organismal Systems' pathways, and 'KEGGdisease' for 'Human Diseases' pathways), 'REACTOME' for REACTOME pathways or 'REACTOME_x' for its sub-ontologies (where x can be 'CellCellCommunication', 'CellCycle', 'CellularResponsesToExternalStimuli', 'ChromatinOrganization', 'CircadianClock', 'DevelopmentalBiology', 'DigestionAndAbsorption', 'Disease', 'DNARepair', 'DNAReplication', 'ExtracellularMatrixOrganization', 'GeneExpression(Transcription)', 'Hemostasis', 'ImmuneSystem', 'Metabolism', 'MetabolismOfProteins', 'MetabolismOfRNA', 'Mitophagy', 'MuscleContraction', 'NeuronalSystem', 'OrganelleBiogenesisAndMaintenance', 'ProgrammedCellDeath', 'Reproduction', 'SignalTransduction', 'TransportOfSmallMolecules', 'VesicleMediatedTransport'), and the molecular signatures database (Msigdb, including "MsigdbH", "MsigdbC1", "MsigdbC2CGP", "MsigdbC2CPall", "MsigdbC2CP", "MsigdbC2KEGG", "MsigdbC2REACTOME", "MsigdbC2BIOCARTA", "MsigdbC3TFT", "MsigdbC3MIR", "MsigdbC4CGN", "MsigdbC4CM", "MsigdbC5BP", "MsigdbC5MF", "MsigdbC5CC", "MsigdbC6", "MsigdbC7"), and the SIFTS database ("SIFTS2GOBP" for Gene Ontology Biological Process, "SIFTS2GOMF" for Gene Ontology Molecular Function, "SIFTS2GOCC" for Gene Ontology Cellular Component), and 'EnrichrX' for Enrichr libraries (where X can be "AchillesFitnessD","AchillesFitnessI","ARCHS4Cells","ARCHS4Tissues","BioCarta","ChEA","ConsensusTFs","dbGaP","DSigDB","EncodeTF","HumanGeneAtlas","huMAP","JensenDiseases","JensenTissues","KEGG","NCIpathway","OMIM","OMIMexpanded","Panther","Reactome","TFlof","TFpert","TissueHumanProteomeMap","TissueProteomicsDB","WikiPathways")

ontology.customised

an object 'GS'. Higher priority over 'ontology' above. Required, otherwise it will return NULL

anno.identity

identity for gene annotations. It can be "GeneID" for Gene ID and "Symbol" for gene symbol. Does not support the customised ontology

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display

RData.location

the characters to tell the location of built-in RData files. See xRDataLoader for details

Value

an object of class "aOnto", a list with two components: an igraph object 'g' (with graph attributes 'ontology' and 'type' [either 'dag' or 'iso']) and a list 'anno'

See Also

xRDataLoader

Examples

# NOT RUN {
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"

# }
# NOT RUN {
aOnto <- xDefineOntology("HPPA", RData.location=RData.location)

# only support internally (please contact us if you would like to use)
aOnto <- xDefineOntology("REACTOME_ImmuneSystem",
RData.location=RData.location)
aOnto <- xDefineOntology("KEGGenvironmental",
RData.location=RData.location)
aOnto <- xDefineOntology("CGL", RData.location=RData.location)

# advanced use: customisation
GS <- xRDataLoader('org.Mm.egKEGG', RData.location=RData.location)
res <- xDefineOntology(ontology.customised=GS)
# }