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R/xDefineOntology.r
In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Defines functions
xDefineOntology
Documented in
xDefineOntology
#' Function to define ontology and its annotations
#'
#' \code{xDefineOntology} is supposed to define ontology and its annotations. It returns an object of class "aOnto".
#'
#' @param 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")
#' @param ontology.customised an object 'GS'. Higher priority over 'ontology' above. Required, otherwise it will return NULL
#' @param anno.identity identity for gene annotations. It can be "GeneID" for Gene ID and "Symbol" for gene symbol. Does not support the customised ontology
#' @param verbose logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display
#' @param RData.location the characters to tell the location of built-in RData files. See \code{\link{xRDataLoader}} for details
#' @param guid a valid (5-character) Global Unique IDentifier for an OSF project. See \code{\link{xRDataLoader}} for details
#' @return
#' 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'
#' @note none
#' @export
#' @seealso \code{\link{xRDataLoader}}
#' @include xDefineOntology.r
#' @examples
#' # Load the XGR package and specify the location of built-in data
#' library(XGR)
#' RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
#'
#' \dontrun{
#' 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)
#' }
xDefineOntology <- function(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", guid=NULL)
{
## match.arg matches arg against a table of candidate values as specified by choices, where NULL means to take the first one
anno.identity <- match.arg(anno.identity)
ontology <- ontology[1]
# input ontology name
ontology.input <- ontology
g <- NULL
anno <- NULL
if(!is.null(ontology.customised)){
if(class(ontology.customised) == "GS"){
GS <- ontology.customised
## get annotation information
anno <- GS$gs
## construct g
nodes <- data.frame(name=as.character(GS$set_info$setID), term_id=as.character(GS$set_info$setID), term_name=as.character(GS$set_info$name), term_distance=as.character(GS$set_info$distance), term_namespace=as.character(GS$set_info$namespace), stringsAsFactors=F)
nodes <- rbind(nodes, c('root','root','root','root','root'))
relations <- data.frame(from='root', to=nodes$name)
g <- igraph::graph.data.frame(d=relations, directed=T, vertices=nodes)
###############
##### g$type: either dag or iso
g$type <- 'iso'
###############
ontology.input <- 'customised'
}
}else{
if(!is.na(ontology)){
if(verbose){
message(sprintf("Load the ontology %s and its gene annotations (%s) ...", ontology, as.character(Sys.time())), appendLF=T)
}
#########
## load GS information
## flag the simplified version of PS
flag_PS2 <- FALSE
if(ontology=="PS2"){
flag_PS2 <- TRUE
ontology <- "PS"
}
## flag the simplified version of REACTOME
flag_REACTOME <- FALSE
if(grepl('REACTOME_', ontology)){
flag_REACTOME <- TRUE
ontology_REACTOME <- ontology
ontology <- "REACTOME"
}
GS <- xRDataLoader(paste('org.Hs.eg', ontology, sep=''), RData.location=RData.location, guid=guid, verbose=verbose)
################
if(flag_PS2){
tmp <- as.character(unique(GS$set_info$name))
inds <- sapply(tmp,function(x) which(GS$set_info$name==x))
## new set_info
set_info <- data.frame()
for(i in 1:length(inds)){
set_info<- rbind(set_info,as.matrix(GS$set_info[max(inds[[i]]),]))
}
## new gs
gs <- list()
for(i in 1:length(inds)){
gs[[i]] <- unlist(GS$gs[inds[[i]]], use.names=F)
}
names(gs) <- rownames(set_info)
## new GS
GS$set_info <- set_info
GS$gs <- gs
}
if(flag_REACTOME){
flag <- unlist(strsplit(ontology_REACTOME, '_'))[2]
if(flag %in% GS$set_info$namespace){
## new GS
GS$set_info <- GS$set_info[GS$set_info$namespace==flag, ]
ind <- match(names(GS$gs), GS$set_info$setID)
GS$gs <- GS$gs[!is.na(ind)]
}
}
################
#########
## get annotation information
anno <- GS$gs
## replace EntrezGenes with gene symbols
if(anno.identity=="Symbol"){
## load Enterz Gene information
EG <- xRDataLoader(RData.customised=paste('org.Hs.eg', sep=''), RData.location=RData.location, guid=guid, verbose=verbose)
## anno_symbols
anno_symbols <- lapply(anno,function(x){
xGeneID2Symbol(x, org=EG, details=F, verbose=F)
})
anno <- anno_symbols
}
#########
## get ontology information
## check the eligibility for the ontology
all.ontologies <- c("GOBP","GOMF","GOCC","DO","HPPA","HPMI","HPCM","HPMA","MP","EF","SIFTS2GOBP","SIFTS2GOMF","SIFTS2GOCC","REACTOME")
flag_ontology <- ontology %in% all.ontologies
if(flag_ontology){
#######################################
ontology <- gsub('^SIFTS2','',ontology)
#######################################
g <- xRDataLoader(RData.customised=paste('ig.', ontology, sep=''), RData.location=RData.location, guid=guid, verbose=verbose)
if(is.null(V(g)$term_namespace)){
V(g)$term_namespace <- ontology
}
#######################################
## restricted to those with annotations for the simplified version of REACTOME
if(flag_REACTOME){
if(0){
g <- dnet::dDAGinduce(g, nodes_query=GS$set_info$setID, path.mode="all_paths")
}else{
ind <- match(V(g)$name, GS$set_info$setID)
vids <- V(g)$name[!is.na(ind)]
neighs.in <- igraph::neighborhood(g, order=vcount(g), nodes=vids, mode="in")
neighbors <- unique(names(unlist(neighs.in)))
g <- dnet::dNetInduce(g, nodes_query=neighbors, knn=0, remove.loops=TRUE, largest.comp=T)
#g <- delete_vertices(g, V(g)$term_name!=unlist(strsplit(ontology_REACTOME, '_'))[2])
}
}
#######################################
###############
##### g$type: either dag or iso
g$type <- 'dag'
###############
}else{
## construct g
nodes <- data.frame(name=as.character(GS$set_info$setID), term_id=as.character(GS$set_info$setID), term_name=as.character(GS$set_info$name), term_distance=as.character(GS$set_info$distance), term_namespace=as.character(GS$set_info$namespace), stringsAsFactors=F)
nodes <- rbind(nodes, c('root','root','root','root','root'))
relations <- data.frame(from='root', to=nodes$name)
g <- igraph::graph.data.frame(d=relations, directed=T, vertices=nodes)
###############
##### g$type: either dag or iso
g$type <- 'iso'
###############
}
}
}
## append graph attribute 'ontology'
g$ontology <- ontology.input
# object 'aOnto'
aOnto <- list(g = g,
anno = anno
)
class(aOnto) <- "aOnto"
invisible(aOnto)
}
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XGR documentation built on Jan. 8, 2020, 5:06 p.m.
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Defines functions xDefineOntology
Documented in xDefineOntology
#' Function to define ontology and its annotations
#'
#' \code{xDefineOntology} is supposed to define ontology and its annotations. It returns an object of class "aOnto".
#'
#' @param 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")
#' @param ontology.customised an object 'GS'. Higher priority over 'ontology' above. Required, otherwise it will return NULL
#' @param anno.identity identity for gene annotations. It can be "GeneID" for Gene ID and "Symbol" for gene symbol. Does not support the customised ontology
#' @param verbose logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display
#' @param RData.location the characters to tell the location of built-in RData files. See \code{\link{xRDataLoader}} for details
#' @param guid a valid (5-character) Global Unique IDentifier for an OSF project. See \code{\link{xRDataLoader}} for details
#' @return
#' 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'
#' @note none
#' @export
#' @seealso \code{\link{xRDataLoader}}
#' @include xDefineOntology.r
#' @examples
#' # Load the XGR package and specify the location of built-in data
#' library(XGR)
#' RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
#'
#' \dontrun{
#' 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)
#' }
xDefineOntology <- function(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", guid=NULL)
{
## match.arg matches arg against a table of candidate values as specified by choices, where NULL means to take the first one
anno.identity <- match.arg(anno.identity)
ontology <- ontology[1]
# input ontology name
ontology.input <- ontology
g <- NULL
anno <- NULL
if(!is.null(ontology.customised)){
if(class(ontology.customised) == "GS"){
GS <- ontology.customised
## get annotation information
anno <- GS$gs
## construct g
nodes <- data.frame(name=as.character(GS$set_info$setID), term_id=as.character(GS$set_info$setID), term_name=as.character(GS$set_info$name), term_distance=as.character(GS$set_info$distance), term_namespace=as.character(GS$set_info$namespace), stringsAsFactors=F)
nodes <- rbind(nodes, c('root','root','root','root','root'))
relations <- data.frame(from='root', to=nodes$name)
g <- igraph::graph.data.frame(d=relations, directed=T, vertices=nodes)
###############
##### g$type: either dag or iso
g$type <- 'iso'
###############
ontology.input <- 'customised'
}
}else{
if(!is.na(ontology)){
if(verbose){
message(sprintf("Load the ontology %s and its gene annotations (%s) ...", ontology, as.character(Sys.time())), appendLF=T)
}
#########
## load GS information
## flag the simplified version of PS
flag_PS2 <- FALSE
if(ontology=="PS2"){
flag_PS2 <- TRUE
ontology <- "PS"
}
## flag the simplified version of REACTOME
flag_REACTOME <- FALSE
if(grepl('REACTOME_', ontology)){
flag_REACTOME <- TRUE
ontology_REACTOME <- ontology
ontology <- "REACTOME"
}
GS <- xRDataLoader(paste('org.Hs.eg', ontology, sep=''), RData.location=RData.location, guid=guid, verbose=verbose)
################
if(flag_PS2){
tmp <- as.character(unique(GS$set_info$name))
inds <- sapply(tmp,function(x) which(GS$set_info$name==x))
## new set_info
set_info <- data.frame()
for(i in 1:length(inds)){
set_info<- rbind(set_info,as.matrix(GS$set_info[max(inds[[i]]),]))
}
## new gs
gs <- list()
for(i in 1:length(inds)){
gs[[i]] <- unlist(GS$gs[inds[[i]]], use.names=F)
}
names(gs) <- rownames(set_info)
## new GS
GS$set_info <- set_info
GS$gs <- gs
}
if(flag_REACTOME){
flag <- unlist(strsplit(ontology_REACTOME, '_'))[2]
if(flag %in% GS$set_info$namespace){
## new GS
GS$set_info <- GS$set_info[GS$set_info$namespace==flag, ]
ind <- match(names(GS$gs), GS$set_info$setID)
GS$gs <- GS$gs[!is.na(ind)]
}
}
################
#########
## get annotation information
anno <- GS$gs
## replace EntrezGenes with gene symbols
if(anno.identity=="Symbol"){
## load Enterz Gene information
EG <- xRDataLoader(RData.customised=paste('org.Hs.eg', sep=''), RData.location=RData.location, guid=guid, verbose=verbose)
## anno_symbols
anno_symbols <- lapply(anno,function(x){
xGeneID2Symbol(x, org=EG, details=F, verbose=F)
})
anno <- anno_symbols
}
#########
## get ontology information
## check the eligibility for the ontology
all.ontologies <- c("GOBP","GOMF","GOCC","DO","HPPA","HPMI","HPCM","HPMA","MP","EF","SIFTS2GOBP","SIFTS2GOMF","SIFTS2GOCC","REACTOME")
flag_ontology <- ontology %in% all.ontologies
if(flag_ontology){
#######################################
ontology <- gsub('^SIFTS2','',ontology)
#######################################
g <- xRDataLoader(RData.customised=paste('ig.', ontology, sep=''), RData.location=RData.location, guid=guid, verbose=verbose)
if(is.null(V(g)$term_namespace)){
V(g)$term_namespace <- ontology
}
#######################################
## restricted to those with annotations for the simplified version of REACTOME
if(flag_REACTOME){
if(0){
g <- dnet::dDAGinduce(g, nodes_query=GS$set_info$setID, path.mode="all_paths")
}else{
ind <- match(V(g)$name, GS$set_info$setID)
vids <- V(g)$name[!is.na(ind)]
neighs.in <- igraph::neighborhood(g, order=vcount(g), nodes=vids, mode="in")
neighbors <- unique(names(unlist(neighs.in)))
g <- dnet::dNetInduce(g, nodes_query=neighbors, knn=0, remove.loops=TRUE, largest.comp=T)
#g <- delete_vertices(g, V(g)$term_name!=unlist(strsplit(ontology_REACTOME, '_'))[2])
}
}
#######################################
###############
##### g$type: either dag or iso
g$type <- 'dag'
###############
}else{
## construct g
nodes <- data.frame(name=as.character(GS$set_info$setID), term_id=as.character(GS$set_info$setID), term_name=as.character(GS$set_info$name), term_distance=as.character(GS$set_info$distance), term_namespace=as.character(GS$set_info$namespace), stringsAsFactors=F)
nodes <- rbind(nodes, c('root','root','root','root','root'))
relations <- data.frame(from='root', to=nodes$name)
g <- igraph::graph.data.frame(d=relations, directed=T, vertices=nodes)
###############
##### g$type: either dag or iso
g$type <- 'iso'
###############
}
}
}
## append graph attribute 'ontology'
g$ontology <- ontology.input
# object 'aOnto'
aOnto <- list(g = g,
anno = anno
)
class(aOnto) <- "aOnto"
invisible(aOnto)
}
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Any scripts or data that you put into this service are public.
R Package Documentation
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