R/parseXML.R
In sandraTL/PathQuant: Annotation of gene-metabolite pairs using topology of KEGG metabolic pathway maps
# This function extract from KGML a list of metabolites (id and name) that
# makes the nodes of the graph ** some metablite can from more than 1 node,
# which is why the id of the nodes is not the name of the metabolite.
# data.frame (id, keggId)
getListNodeFromKGML <- function(pathwayId) {
# print("getListNodeFromKGML")
xmltop <- getKGMLRootNode(pathwayId);
nodeListId <- XML::xpathSApply(xmltop,
"//entry[@type = 'compound']",
function(x) (XML::xmlAttrs(x))['id']);
nodeListCpd <- XML::xpathSApply(xmltop,
"//entry[@type = 'compound']",
function(x) (XML::xmlAttrs(x))['name']);
nodeListColor <- XML::xpathSApply(xmltop,
"//entry[@type = 'compound']//graphics",
function(x) (XML::xmlAttrs(x))['fgcolor'])
nodeDF <- data.frame(kgmlId = as.vector(unlist(nodeListId)),
keggId = as.vector(unlist(nodeListCpd)),
color = as.vector(unlist(nodeListColor)));
nodeDF <- correctKeggIdString(nodeDF);
return <- nodeDF;
}
# This function creates a data.frame containing the first part of our edge list
# the "gene" reactions
# data.frame(kgmlIdSubstratre, kgmlIdProduct, substrateName, productName,
# kgmlIdReaction, reactionName, reactionType)
getListReactionFromKGML <- function(pathwayId) {
#print("getListReactionFromKGML")
#gives content of root
xmltop <- getKGMLRootNode(pathwayId);
reactionIdNodes <- XML::getNodeSet(xmltop, "//reaction");
reactionId <- lapply(reactionIdNodes,
function(x) XML::xmlAttrs(x)['id']);
reactionName <- lapply(reactionIdNodes,
function(x) XML::xmlAttrs(x)['name']);
reactionType <- lapply(reactionIdNodes,
function(x) XML::xmlAttrs(x)['type']);
substrateId <- lapply(reactionIdNodes, XML::xpathApply,path = './substrate',
function(x) XML::xmlAttrs(x)['id']);
substrateName <- lapply(reactionIdNodes, XML::xpathApply,
path = './substrate',
function(x) XML::xmlAttrs(x)['name']);
productId <- lapply(reactionIdNodes, XML::xpathApply,
path = './product',
function(x) XML::xmlAttrs(x)['id']);
productName <- lapply(reactionIdNodes, XML::xpathApply,
path = './product',
function(x) XML::xmlAttrs(x)['name']);
if(length(reactionIdNodes) > 0) {
max1 <- max(lengths(substrateId));
max2 <- max(lengths(productId));
max3 <- max(lengths(substrateName));
max4 <- max(lengths(productName));
max5 <- max(lengths(reactionId));
max6 <- max(lengths(reactionType));
max7 <- max(lengths(reactionName));
sum <- (max1 + max2 + max3 +max4 + max5 + max6 +max7);
# print(substrateId)
# print(productId)
# print(substrateName)
# print(productName)
# print(reactionId)
# print(reactionType)
# print(reactionName)
# print(length(substrateId));
# print(length(productId));
# print(length(substrateName));
# print(length(productName));
# print(length(reactionId));
# print(length(reactionType));
# print(length(reactionName));
# print(pathwayId)
if(sum > 7) {
reactionList <- do.call(rbind.data.frame,
mapply(cbind,
"substrateId" = substrateId,
"productId" = productId,
"substrateName" = substrateName,
"productName" = productName,
"reactionId" = reactionId,
"reactionType" = reactionType,
"reactionName" = reactionName
));
} else if(sum == 7) {
reactionList <- data.frame(cbind(
"substrateId" = as.numeric(unlist(substrateId)),
"productId" = as.numeric(unlist(productId)),
"substrateName" = as.character(unlist(substrateName)),
"productName" = as.character(unlist(productName)),
"reactionId" = as.numeric(reactionId),
"reactionType" = reactionType,
"reactionName" = reactionName
));
}
} else {
reactionList <- data.frame();
}
return <- reactionList;
}
getListOfUniqueHSAGeneId <- function(pathwayId){
print("getListOfUniqueHSAGeneId")
gene.list <- getListEdgeFromGeneKGML(pathwayId)$ko
gene.list <- paste(gene.list, collapse = " ")
gene.list <- strsplit(gene.list, " ")
gene.list <- gene.list[[1]][!duplicated(gene.list[[1]])]
return <- gene.list
}
getListOfUniqueMetabolite <- function(pathwayId){
print("getListOfUniqueMetabolite")
metabo.list <- getListNodeFromKGML(pathwayId)$keggId
metabo.list <- paste(metabo.list, collapse = " ")
metabo.list <- strsplit(metabo.list, " ")
metabo.list <- metabo.list[[1]][!duplicated(metabo.list[[1]])]
return <- metabo.list
}
getListUniqueMetaboliteInReactions <- function(pathwayId){
print("getListUniqueMetaboliteInReactions")
reac.sub.list <- getListReactionFromKGML(pathwayId)$substrateName
reac.prod.list <- getListReactionFromKGML(pathwayId)$productName
reac.sub.list <- paste(reac.sub.list, collapse = " ")
reac.prod.list <- paste(reac.prod.list, collapse = " ")
reac.me.list <- paste(reac.sub.list, reac.prod.list, collapse = " ")
reac.me.list <- strsplit(reac.me.list, " ")
reac.me.list <- reac.me.list[[1]][!duplicated(reac.me.list[[1]])]
return <- reac.me.list
}
# This function extract from KGML a list of reaction of entry-type "gene"
# Returns a dataFrame object : id, entryId, reaction, ko
getListEdgeFromGeneKGML <- function(pathwayId) {
# print("getListEdgeFromGeneKGML")
# get the root of the KGML document
xmltop <- getKGMLRootNode(pathwayId);
# Get value of atributes (id, name(ko) and reaction) of entry of type
# ortholog, some don't have reaction argument thus won't have an edge in
# our final graph they will have NA in data.frame.
edgeListId <- XML::xpathSApply(xmltop, "//entry[@type = 'gene']",
function(x) (XML::xmlAttrs(x))['id']);
edgeListKo <- XML::xpathSApply(xmltop, "//entry[@type = 'gene']",
function(x) (XML::xmlAttrs(x))['name']);
edgeListReaction <- XML::xpathSApply(xmltop, "//entry[@type = 'gene']",
function(x) (XML::xmlAttrs(x))['reaction']);
edgeDF <- data.frame("reactionId" = as.vector(as.character(edgeListId)),
"reactions" = as.vector(as.character(edgeListReaction)),
"type" = as.vector("gene"),
"ko" = as.vector(as.character(edgeListKo)));
return <- edgeDF;
}
# This function extract from KGML a list of reaction of entry-type "gene"
# Returns a dataFrame object : id, entryId, reaction, ko
getListOrthologGeneFromKGML <- function(pathwayId) {
# print("getListOrthologGeneFromKGML")
# get the root of the KGML document
xmltop <- getKGMLRootNode(pathwayId);
# Get value of atributes (id, name(ko) and reaction) of entry of type
# ortholog, some don't have reaction argument thus won't have an edge in
# our final graph they will have NA in data.frame.
orthologListId <- XML::xpathSApply(xmltop,
"//entry[@type = 'ortholog']",
function(x) (XML::xmlAttrs(x))['id']);
orthologListKo <- XML::xpathSApply(xmltop,
"//entry[@type = 'ortholog']",
function(x) (XML::xmlAttrs(x))['name']);
orthologListReaction <- XML::xpathSApply(xmltop,
"//entry[@type = 'ortholog']",
function(x) (XML::xmlAttrs(x))['reaction']);
orthologDF <- data.frame(
"reactionId" = as.vector(as.character(orthologListId)),
"reactions" = as.vector(as.character(orthologListReaction)),
"ko" = as.vector(as.character(orthologListKo)),
"x" = as.vector(rep(-1, length(orthologListReaction))),
"y" = as.vector(rep(-1, length(orthologListReaction)))
);
for(row in 1:length(orthologDF[,1])){
id <- orthologDF[row,1]
coords <- XML::xpathSApply(xmltop,
"//entry[@id = id]//graphics",
function(x) (XML::xmlAttrs(x))['coords']);
if(length(coords) == 1){
orthologDF[row,4] <- coords;
}
}
orthologListNameCoords <- XML::xpathSApply(xmltop, "//entry[@type = 'ortholog']//graphics",
function(x) (XML::xmlAttrs(x))['name']);
orthologListCoords <- XML::xpathSApply(xmltop, "//entry[@type = 'ortholog']//graphics",
function(x) (XML::xmlAttrs(x))['coords']);
orthologCoords <- data.frame("nameCoords" =as.vector(as.character(orthologListNameCoords)),
"coords" = as.vector(as.character(orthologListCoords)));
}
getKGMLRootNode <- function(pathwayId){
# get the root of the KGML document
# print("getKGMLRootNode")
pathFile <- toStringPathFile(pathwayId);
if(is.na(file.info(pathFile)$size)== FALSE){
xmlfile <- XML::xmlParse(pathFile);
xmltop <- XML::xmlRoot(xmlfile); # gives content of root
}else{
getPathwayKGML(pathwayId)
xmlfile <- XML::xmlParse(pathFile);
xmltop <- XML::xmlRoot(xmlfile); # gives content of root
}
return <- xmltop;
}
toStringPathFile <- function(pathwayId){
# print("toStringPathFile")
# concatenation of pathwayId to set swdir for the xml
s2 <- toString(pathwayId);
s3 <- ".txt"
pathFile <- paste(s2, s3, sep="");
return <- pathFile;
}
getPathCommonNames <- function(path){
print("getPathCommonNames")
pathSplit <- strsplit(as.character(path[1,]), " ")
for(i in 1:length(pathSplit[[1]])){
if(substring(pathSplit[[1]][i],1,1) == "C" && nchar(pathSplit[[1]][i]) == 6){
pathSplit[[1]][i] <- getCommonNames(pathSplit[[1]][i], "metabolite")
}else if(substring(pathSplit[[1]][i],1,4) == "hsa:"){
pathSplit[[1]][i] <- getCommonNames(pathSplit[[1]][i], "gene")
}
}
pathSplit <- do.call(paste, c(as.list(pathSplit[[1]]), sep=" "));
return <- pathSplit;
}
getCommonNames <- function(vectorOfKEGGIds, type = c("gene","metabolite")){
# print("getCommonNames")
count <- 1;
### Vérifiez la connection internet
if(length(vectorOfKEGGIds) > 0 ){
# analysis of submaps - beggining
names <- character();
while(count <= length(vectorOfKEGGIds)){
names1<- getNames(vectorOfKEGGIds[count], type)
names <- append(names,names1)
count <- count + 1;
}
}
return <- names;
}
getNames <- function(keggId, type){
# print("getNames")
# print(keggId)
### Vérifiez la connection internet
name <- NULL;
if (is.na(keggId)) {
name <- NA;
} else {
url <- getKEGGInfoUrl(keggId)
foundName <- FALSE;
allLines <- readLines(url);
i <- 1;
while(foundName == FALSE){
allLines[i] <- stringr::str_trim(allLines[i], "both")
if(type == "gene"){
tmp <- strsplit(allLines[i], "\\s+|,|;")
if(!is.null(tmp[[1]][1])){
if(tmp[[1]][1] =="NAME"){
name <- tmp[[1]][2]
foundName <- TRUE;
}}
i <- i+1;
}
else if(type == "metabolite"){
tmp <- strsplit(allLines[i], "\\s+|;")
if(!is.null(tmp[[1]][1])){
if(tmp[[1]][1] =="NAME"){
name <- tmp[[1]][2]
foundName <- TRUE;
}}
i <- i+1;
}
}
}
return <- name
}
# trim <- function (x) gsub("^\\s+|\\s+$", "", x)
# getBrites <- function(Associations){
# print("getBrites")
#
# brite<- character();
# # Associations <- Associations[,c(2,5)]
# # Associations <- Associations[!duplicated(Associations),]
# for(j in 1:nrow(Associations)){
#
# url <- getKEGGInfoUrl(Associations[j,3])
#
# foundName <- FALSE;
# allLines <- readLines(url);
# i <- 1;
#
# for(i in 1:length(allLines)){
# temp <- character();
# tmp <- strsplit(allLines[i], "\\s+|;")
# if(!is.null(tmp[[1]][1])){
#
# if(tmp[[1]][1] =="BRITE"){
# foundName <- TRUE;
# if(tmp[[1]][2] == "Compounds"){
# temp <- paste(trim(allLines[i+1]),
# "-", trim(allLines[i+2]),sep = " ");
#
# }else if(tmp[[1]][2] == "Anatomical"){
# temp <-paste(tmp[[1]][2],"-",trim(allLines[i+4]),sep = " ")
# }else if(tmp[[1]][2] == "Pharmaceutical"){
# temp <-paste(tmp[[1]][2],tmp[[1]][3],
# sep = " ")
# }else if(tmp[[1]][2] == "Phytochemical"){
# temp <-paste(tmp[[1]][2],"-",trim(allLines[i+1]),
# sep = " ")
# }else if(tmp[[1]][2] == "Pesticides"){
# temp <-paste(tmp[[1]][2],"-",trim(allLines[i+1]),
# sep = " ")
# }else{
# temp <-paste(tmp[[1]][2],"-",trim(allLines[i+1]), sep = " ")
# }
#
# }
# brite <- append(brite,temp)
# }
#
# }
#
# if(foundName==FALSE){
# temp <- "not classified by KEGG yet"
#
# brite <- append(brite,temp)
# }
#
# }
#
# Associations <- cbind(Associations, "Chemical Class" = as.vector(brite))
# return <- Associations;
# }
getKEGGInfoUrl <- function(keggId){
# print("getKEGGInfoUrl")
url <- "http://rest.kegg.jp/get/"
url <- paste(url, keggId, sep = "")
return <- url;
}
#
# getFirstLevelSubMaps <- function(pathwayId) {
#
# print("getFirstLevelSubMaps")
#
# xmltop <- getKGMLRootNode(pathwayId);
#
#
# mapId <- XML::xpathSApply(xmltop, "//entry[@type = 'map']",
# function(x) (XML::xmlAttrs(x))['name']);
#
# return <- mapId
# }
#
#
#
#
#
#
# isAllGeneOfSubGraphsInKEGGOverview <- function(subGraphId){
#
# print("isAllGeneOfSubGraphsInKEGGOverview")
#
# overviewGeneList <- KEGGREST::keggLink("genes", "hsa01100")
#
#
# subGraphGeneList <- KEGGREST::keggLink("genes", subGraphId)
#
# notInOverview <- c();
# for(i in 1:length(subGraphGeneList)){
#
# subGraphGene_Grep<- paste("\\",subGraphGeneList[[i]],"\\b",sep="")
#
# r <- grep(subGraphGene_Grep, overviewGeneList);
#
# if(length(r) == 0){
# notInOverview <- c(notInOverview,subGraphGeneList[[i]])
# }
#
# }
#
# return(notInOverview)
#
# }
#
# allSubMapsMetaboliteAnalysis <- function(){
#
# print("allSubMapsMetaboliteAnalysis")
#
# allSubMaps <- getFirstLevelSubMaps("hsa01100")
# analysisResults<- NULL;
#
# for(i in 1:length(allSubMaps)){
# allSubMaps[[i]] <- gsub("path:", "", allSubMaps[[i]])
#
# if(substr(allSubMaps[[i]],1,3) == "hsa"){
# mapSubMapId <- gsub("hsa", "map", allSubMaps[[i]])
# numberGeneOfSubMap <- length(KEGGREST::keggLink("cpd",mapSubMapId))
#
# notInOverview <- isAllMetaboliteOfSubGraphsInKEGGOverview(mapSubMapId)
# subMapName <- KEGGREST::keggGet(allSubMaps[[i]])[[1]]$NAME
# subMapClass <- KEGGREST::keggGet(allSubMaps[[i]])[[1]]$CLASS
#
# if(length(notInOverview) == 0){
# notInOverview <- NA;
# numberGeneNotInOverview <- 0;
# }else{
# numberGeneNotInOverview <- length(notInOverview)
# notInOverview <- paste(notInOverview, collapse = ',')
# }
# analysisResults <-rbind(analysisResults,
# c(subMapKEGGId = as.vector(allSubMaps[[i]]),
# subMapName = as.vector(subMapName),
# subMapClass = as.vector(subMapClass),
# numberMetaboliteOfSubMap = as.vector(numberGeneOfSubMap),
# numberMetaboliteNotInOverview = as.vector(numberGeneNotInOverview),
# metaboliteNotInOverviewKEGGId = as.vector(notInOverview)))
#
#
# }
# }
#
# return <- analysisResults;
#
# }
#
# isAllMetaboliteOfSubGraphsInKEGGOverview <- function(subGraphId){
#
# print("isAllMetaboliteOfSubGraphsInKEGGOverview")
#
# overviewMetaboliteList <- KEGGREST::keggLink("cpd", "map01100")
#
#
# subGraphMetaboliteList <- KEGGREST::keggLink("cpd", subGraphId)
#
# notInOverview <- c();
#
# if(length(subGraphMetaboliteList)>0){
# for(i in 1:length(subGraphMetaboliteList)){
#
# subGraphMetabolite_Grep<-
# paste("\\",subGraphMetaboliteList[[i]],"\\b",sep="")
#
# r <- grep(subGraphMetabolite_Grep, overviewMetaboliteList);
#
# if(length(r) == 0){
# notInOverview <- c(notInOverview,subGraphMetaboliteList[[i]])
# }
#
# }
# }
# return(notInOverview)
#
# }
#
# allSubMapsGeneAnalysis <- function(){
#
# print("allSubMapsGeneAnalysis")
#
# allSubMaps <- getFirstLevelSubMaps("hsa01100")
# analysisResults<- NULL;
# for(i in 1:length(allSubMaps)){
# allSubMaps[[i]] <- gsub("path:", "", allSubMaps[[i]])
# if(substr(allSubMaps[[i]],1,3) == "hsa"){
# numberGeneOfSubMap <- length(KEGGREST::keggLink("genes",allSubMaps[[i]]))
#
# notInOverview <- isAllGeneOfSubGraphsInKEGGOverview(allSubMaps[[i]])
# subMapName <- KEGGREST::keggGet(allSubMaps[[i]])[[1]]$NAME
# subMapClass <- KEGGREST::keggGet(allSubMaps[[i]])[[1]]$CLASS
#
# if(length(notInOverview) == 0){
# notInOverview <- NA;
# numberGeneNotInOverview <- 0;
# }else{
# numberGeneNotInOverview <- length(notInOverview)
# notInOverview <- paste(notInOverview, collapse = ',')
# }
# analysisResults <-rbind(analysisResults,
# c(subMapKEGGId = as.vector(allSubMaps[[i]]),
# subMapName = as.vector(subMapName),
# subMapClass = as.vector(subMapClass),
# numberGeneOfSubMap = as.vector(numberGeneOfSubMap),
# numberGeneNotInOverview = as.vector(numberGeneNotInOverview),
# geneNotInOverviewKEGGId = as.vector(notInOverview)))
#
#
#
# }
# }
#
# return <- analysisResults;
#
# }
#
# getHMDBByKEGGId <-function(keggId) {
#
# print("getHMDBByKEGGId")
#
# files <- list.files("./hmdb_metabolites")
# files <- files[-1]
#
# res <- lapply(keggId, function(i)
#
# lapply(files, function(j)
# compareWihtNodeKeggId(j,i)))
#
#
# return <- res;
#
# }
#
# getHMDBInfo <- function(){
#
# print("getHMDBInfo")
#
# files <- list.files("/Users/sandra/Documents/workspaceMetabolomics/hmbdParser/hmdb_metabolites")
# files <- files[-1]
#
# hmdb <- getHMDBIds(files)
#
# kegg_ids <- lapply(files, function(j) getKeggIdByHMDB(j))
# super_class <- lapply(files, function(j) getSuperClassByHMDB(j))
# class <- lapply(files, function(j) getClassByHMDB(j))
# hmdb_infoDF <-data.frame(cbind("hmdb_Id" = as.vector(hmdb),
# "kegg_Id" = as.vector(kegg_ids),
# "super_class" = as.vector(super_class),
# "class" = as.vector(class)))
# exportHMDBInfo(hmdb_infoDF)
# return <- hmdb_infoDF
# }
#
#
# getKeggIdByHMDB <- function(fileName){
#
# print("getKeggIdByHMDB")
#
# fileName <- paste("/Users/sandra/Documents/workspaceMetabolomics/hmbdParser/hmdb_metabolites/", fileName, sep="")
# doc1 <- XML::xmlParse(fileName);
# node_kegg_id <- XML::xpathApply(doc1, "//kegg_id")
#
# kegg_id <- XML::xmlSApply(node_kegg_id, XML::xmlValue)
#
# if(nchar(kegg_id) == 0) kegg_id <- NA;
#
# return <- kegg_id;
# }
#
# getSuperClassByHMDB <- function(fileName){
#
# print("getSuperClassByHMDB")
#
# fileName <- paste("/Users/sandra/Documents/workspaceMetabolomics/hmbdParser/hmdb_metabolites/", fileName, sep="")
# doc1 <- XML::xmlParse(fileName);
#
# node_super_class <- XML::xpathApply(doc1, "//super_class")
#
# super_class <- XML::xmlSApply(node_super_class, XML::xmlValue)
#
# if(nchar(super_class) == 0) super_class <- NA
#
# return <- super_class
# }
#
# getClassByHMDB <- function(fileName){
#
# print("getClassByHMDB")
#
# fileName <- paste("/Users/sandra/Documents/workspaceMetabolomics/hmbdParser/hmdb_metabolites/", fileName, sep="")
# doc1 <- XML::xmlParse(fileName);
#
# node_class <- XML::xpathApply(doc1, "//class")
#
# class <- XML::xmlSApply(node_class, XML::xmlValue)
#
# if(nchar(class) == 0) class <- NA;
#
# return <- class;
# }
#Data <- ldply(files,parse_xml)
#
# getHMDBIds <- function(fileList){
#
# print("getHMDBIds")
# finalList <- lapply(fileList, function(x) gsub( ".xml", "",x))
# return <- finalList;
#
# }
#
# exportHMDBInfo <- function(hmdb_infoDF){
#
# print("exportHMDBInfo")
# hmdb_infoDF <- data.frame(lapply(hmdb_infoDF, as.character), stringsAsFactors=FALSE)
# exportDFtoTxt(hmdb_infoDF, "hmdb_info")
# }
#
#
# getHMDBIdByKEggId <- function(keggIdList){
#
# print("getHMDBIdByKEggId")
#
# res <- importTXTtoDF("hmdb_info.txt")
#
# r <-lapply(keggIdList, function(x) subset(res, res[2] == x));
#
# r <- do.call(rbind, r)
#
# r <- prepOutputHMDBIdByKEggId(r);
#
# return <- r[,c(2,1)];
# }
## could also annotate from HMDB database
getSuperClassByKEggId <- function(kegg.id.list){
# print("getSuperClassByKEggId")
# retrieve data from HMDB xml files
hmdb.data <- data.frame(importTXTtoDF("hmdb_info.txt"))
# hmdb.data <- load("")
# print(typeof(hmdb.data))
# print(hmdb.data)
# unlist the data to for lapply
kegg.id.list <- unlist(kegg.id.list)
# print(kegg.id.list)
r <- lapply(kegg.id.list, function(x) {
x.1 <- paste("\\b", x,"\\b",sep="")
if (nrow(hmdb.data[grep(x.1, hmdb.data$kegg_Id),]) == 0) {
data.frame("hmdb_Id" = NA,
"kegg_Id" = x,
"super_class" = NA,
"class" = NA)
# carefull I only took the first line
# but multiple line mean multiple classes that should be
# bind together
} else {
hmdb.data[grep(x.1, hmdb.data$kegg_Id),][1,]
}
});
#bind the results for each compound
r <- do.call(rbind, r)
return <- r[,3];
}
#
# getClassByKEggId <- function(keggIdList){
#
# print("getClassByKEggId")
#
# res <- importTXTtoDF("hmdb_info.txt")
#
# r <-lapply(keggIdList, function(x) subset(res, res[2] == x));
#
# r <- do.call(rbind, r)
#
# # r <- prepOutputHMDBIdByKEggId(r);
#
# return <- r[,c(2,4)];
# }
#
# getAllHMDBbyKeggId <- function(keggIdList){
#
# print("getAllHMDBbyKeggId")
#
# res <- importTXTtoDF("hmdb_info.txt")
#
# r <-lapply(keggIdList, function(x) subset(res, res[2] == x));
#
# r <- do.call(rbind, r)
#
# # r <- prepOutputHMDBIdByKEggId(r);
#
# return <- r;
# }
#
# ## put this in a general data frame help function
# prepOutputHMDBIdByKEggId <- function(metabolitesNamesDF){
#
# print("prepOutputHMDBIdByKEggId")
#
# metabo <- ""
# hmdb_ids <- ""
# df <- data.frame();
#
# for(x in 1:nrow(metabolitesNamesDF)){
# # conditino to get first row
# if(metabo == ""){
# metabo <- metabolitesNamesDF[x,2];
# hmdb_ids <- paste(hmdb_ids, metabolitesNamesDF[x,1])
#
# # conditino get inside rows and combine first colinfo info based on
# # duplicated 2 col
# }else if(!(metabo == as.character(metabolitesNamesDF[x,2]))){
#
# df <- rbind(df, data.frame("keggId" = as.vector(as.character(metabo)),
# "hmdbIds" = as.vector(hmdb_ids)))
# hmdb_ids <- "";
# metabo <- metabolitesNamesDF[x,2]
# hmdb_ids <- paste(hmdb_ids, metabolitesNamesDF[x,1])
#
# }else{
# hmdb_ids <- paste(hmdb_ids, metabolitesNamesDF[x,1])
# }
#
# # ctach last row
# if(x == nrow(metabolitesNamesDF)){
# df <- rbind(df, data.frame("keggId" = as.vector(as.character(metabo)),
# "hmdbIds" = as.vector(hmdb_ids)))
# }
# }
#
#
# return <- df;
#
# }
sandraTL/PathQuant documentation built on May 29, 2019, 1:45 p.m.
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# This function extract from KGML a list of metabolites (id and name) that
# makes the nodes of the graph ** some metablite can from more than 1 node,
# which is why the id of the nodes is not the name of the metabolite.
# data.frame (id, keggId)
getListNodeFromKGML <- function(pathwayId) {
# print("getListNodeFromKGML")
xmltop <- getKGMLRootNode(pathwayId);
nodeListId <- XML::xpathSApply(xmltop,
"//entry[@type = 'compound']",
function(x) (XML::xmlAttrs(x))['id']);
nodeListCpd <- XML::xpathSApply(xmltop,
"//entry[@type = 'compound']",
function(x) (XML::xmlAttrs(x))['name']);
nodeListColor <- XML::xpathSApply(xmltop,
"//entry[@type = 'compound']//graphics",
function(x) (XML::xmlAttrs(x))['fgcolor'])
nodeDF <- data.frame(kgmlId = as.vector(unlist(nodeListId)),
keggId = as.vector(unlist(nodeListCpd)),
color = as.vector(unlist(nodeListColor)));
nodeDF <- correctKeggIdString(nodeDF);
return <- nodeDF;
}
# This function creates a data.frame containing the first part of our edge list
# the "gene" reactions
# data.frame(kgmlIdSubstratre, kgmlIdProduct, substrateName, productName,
# kgmlIdReaction, reactionName, reactionType)
getListReactionFromKGML <- function(pathwayId) {
#print("getListReactionFromKGML")
#gives content of root
xmltop <- getKGMLRootNode(pathwayId);
reactionIdNodes <- XML::getNodeSet(xmltop, "//reaction");
reactionId <- lapply(reactionIdNodes,
function(x) XML::xmlAttrs(x)['id']);
reactionName <- lapply(reactionIdNodes,
function(x) XML::xmlAttrs(x)['name']);
reactionType <- lapply(reactionIdNodes,
function(x) XML::xmlAttrs(x)['type']);
substrateId <- lapply(reactionIdNodes, XML::xpathApply,path = './substrate',
function(x) XML::xmlAttrs(x)['id']);
substrateName <- lapply(reactionIdNodes, XML::xpathApply,
path = './substrate',
function(x) XML::xmlAttrs(x)['name']);
productId <- lapply(reactionIdNodes, XML::xpathApply,
path = './product',
function(x) XML::xmlAttrs(x)['id']);
productName <- lapply(reactionIdNodes, XML::xpathApply,
path = './product',
function(x) XML::xmlAttrs(x)['name']);
if(length(reactionIdNodes) > 0) {
max1 <- max(lengths(substrateId));
max2 <- max(lengths(productId));
max3 <- max(lengths(substrateName));
max4 <- max(lengths(productName));
max5 <- max(lengths(reactionId));
max6 <- max(lengths(reactionType));
max7 <- max(lengths(reactionName));
sum <- (max1 + max2 + max3 +max4 + max5 + max6 +max7);
# print(substrateId)
# print(productId)
# print(substrateName)
# print(productName)
# print(reactionId)
# print(reactionType)
# print(reactionName)
# print(length(substrateId));
# print(length(productId));
# print(length(substrateName));
# print(length(productName));
# print(length(reactionId));
# print(length(reactionType));
# print(length(reactionName));
# print(pathwayId)
if(sum > 7) {
reactionList <- do.call(rbind.data.frame,
mapply(cbind,
"substrateId" = substrateId,
"productId" = productId,
"substrateName" = substrateName,
"productName" = productName,
"reactionId" = reactionId,
"reactionType" = reactionType,
"reactionName" = reactionName
));
} else if(sum == 7) {
reactionList <- data.frame(cbind(
"substrateId" = as.numeric(unlist(substrateId)),
"productId" = as.numeric(unlist(productId)),
"substrateName" = as.character(unlist(substrateName)),
"productName" = as.character(unlist(productName)),
"reactionId" = as.numeric(reactionId),
"reactionType" = reactionType,
"reactionName" = reactionName
));
}
} else {
reactionList <- data.frame();
}
return <- reactionList;
}
getListOfUniqueHSAGeneId <- function(pathwayId){
print("getListOfUniqueHSAGeneId")
gene.list <- getListEdgeFromGeneKGML(pathwayId)$ko
gene.list <- paste(gene.list, collapse = " ")
gene.list <- strsplit(gene.list, " ")
gene.list <- gene.list[[1]][!duplicated(gene.list[[1]])]
return <- gene.list
}
getListOfUniqueMetabolite <- function(pathwayId){
print("getListOfUniqueMetabolite")
metabo.list <- getListNodeFromKGML(pathwayId)$keggId
metabo.list <- paste(metabo.list, collapse = " ")
metabo.list <- strsplit(metabo.list, " ")
metabo.list <- metabo.list[[1]][!duplicated(metabo.list[[1]])]
return <- metabo.list
}
getListUniqueMetaboliteInReactions <- function(pathwayId){
print("getListUniqueMetaboliteInReactions")
reac.sub.list <- getListReactionFromKGML(pathwayId)$substrateName
reac.prod.list <- getListReactionFromKGML(pathwayId)$productName
reac.sub.list <- paste(reac.sub.list, collapse = " ")
reac.prod.list <- paste(reac.prod.list, collapse = " ")
reac.me.list <- paste(reac.sub.list, reac.prod.list, collapse = " ")
reac.me.list <- strsplit(reac.me.list, " ")
reac.me.list <- reac.me.list[[1]][!duplicated(reac.me.list[[1]])]
return <- reac.me.list
}
# This function extract from KGML a list of reaction of entry-type "gene"
# Returns a dataFrame object : id, entryId, reaction, ko
getListEdgeFromGeneKGML <- function(pathwayId) {
# print("getListEdgeFromGeneKGML")
# get the root of the KGML document
xmltop <- getKGMLRootNode(pathwayId);
# Get value of atributes (id, name(ko) and reaction) of entry of type
# ortholog, some don't have reaction argument thus won't have an edge in
# our final graph they will have NA in data.frame.
edgeListId <- XML::xpathSApply(xmltop, "//entry[@type = 'gene']",
function(x) (XML::xmlAttrs(x))['id']);
edgeListKo <- XML::xpathSApply(xmltop, "//entry[@type = 'gene']",
function(x) (XML::xmlAttrs(x))['name']);
edgeListReaction <- XML::xpathSApply(xmltop, "//entry[@type = 'gene']",
function(x) (XML::xmlAttrs(x))['reaction']);
edgeDF <- data.frame("reactionId" = as.vector(as.character(edgeListId)),
"reactions" = as.vector(as.character(edgeListReaction)),
"type" = as.vector("gene"),
"ko" = as.vector(as.character(edgeListKo)));
return <- edgeDF;
}
# This function extract from KGML a list of reaction of entry-type "gene"
# Returns a dataFrame object : id, entryId, reaction, ko
getListOrthologGeneFromKGML <- function(pathwayId) {
# print("getListOrthologGeneFromKGML")
# get the root of the KGML document
xmltop <- getKGMLRootNode(pathwayId);
# Get value of atributes (id, name(ko) and reaction) of entry of type
# ortholog, some don't have reaction argument thus won't have an edge in
# our final graph they will have NA in data.frame.
orthologListId <- XML::xpathSApply(xmltop,
"//entry[@type = 'ortholog']",
function(x) (XML::xmlAttrs(x))['id']);
orthologListKo <- XML::xpathSApply(xmltop,
"//entry[@type = 'ortholog']",
function(x) (XML::xmlAttrs(x))['name']);
orthologListReaction <- XML::xpathSApply(xmltop,
"//entry[@type = 'ortholog']",
function(x) (XML::xmlAttrs(x))['reaction']);
orthologDF <- data.frame(
"reactionId" = as.vector(as.character(orthologListId)),
"reactions" = as.vector(as.character(orthologListReaction)),
"ko" = as.vector(as.character(orthologListKo)),
"x" = as.vector(rep(-1, length(orthologListReaction))),
"y" = as.vector(rep(-1, length(orthologListReaction)))
);
for(row in 1:length(orthologDF[,1])){
id <- orthologDF[row,1]
coords <- XML::xpathSApply(xmltop,
"//entry[@id = id]//graphics",
function(x) (XML::xmlAttrs(x))['coords']);
if(length(coords) == 1){
orthologDF[row,4] <- coords;
}
}
orthologListNameCoords <- XML::xpathSApply(xmltop, "//entry[@type = 'ortholog']//graphics",
function(x) (XML::xmlAttrs(x))['name']);
orthologListCoords <- XML::xpathSApply(xmltop, "//entry[@type = 'ortholog']//graphics",
function(x) (XML::xmlAttrs(x))['coords']);
orthologCoords <- data.frame("nameCoords" =as.vector(as.character(orthologListNameCoords)),
"coords" = as.vector(as.character(orthologListCoords)));
}
getKGMLRootNode <- function(pathwayId){
# get the root of the KGML document
# print("getKGMLRootNode")
pathFile <- toStringPathFile(pathwayId);
if(is.na(file.info(pathFile)$size)== FALSE){
xmlfile <- XML::xmlParse(pathFile);
xmltop <- XML::xmlRoot(xmlfile); # gives content of root
}else{
getPathwayKGML(pathwayId)
xmlfile <- XML::xmlParse(pathFile);
xmltop <- XML::xmlRoot(xmlfile); # gives content of root
}
return <- xmltop;
}
toStringPathFile <- function(pathwayId){
# print("toStringPathFile")
# concatenation of pathwayId to set swdir for the xml
s2 <- toString(pathwayId);
s3 <- ".txt"
pathFile <- paste(s2, s3, sep="");
return <- pathFile;
}
getPathCommonNames <- function(path){
print("getPathCommonNames")
pathSplit <- strsplit(as.character(path[1,]), " ")
for(i in 1:length(pathSplit[[1]])){
if(substring(pathSplit[[1]][i],1,1) == "C" && nchar(pathSplit[[1]][i]) == 6){
pathSplit[[1]][i] <- getCommonNames(pathSplit[[1]][i], "metabolite")
}else if(substring(pathSplit[[1]][i],1,4) == "hsa:"){
pathSplit[[1]][i] <- getCommonNames(pathSplit[[1]][i], "gene")
}
}
pathSplit <- do.call(paste, c(as.list(pathSplit[[1]]), sep=" "));
return <- pathSplit;
}
getCommonNames <- function(vectorOfKEGGIds, type = c("gene","metabolite")){
# print("getCommonNames")
count <- 1;
### Vérifiez la connection internet
if(length(vectorOfKEGGIds) > 0 ){
# analysis of submaps - beggining
names <- character();
while(count <= length(vectorOfKEGGIds)){
names1<- getNames(vectorOfKEGGIds[count], type)
names <- append(names,names1)
count <- count + 1;
}
}
return <- names;
}
getNames <- function(keggId, type){
# print("getNames")
# print(keggId)
### Vérifiez la connection internet
name <- NULL;
if (is.na(keggId)) {
name <- NA;
} else {
url <- getKEGGInfoUrl(keggId)
foundName <- FALSE;
allLines <- readLines(url);
i <- 1;
while(foundName == FALSE){
allLines[i] <- stringr::str_trim(allLines[i], "both")
if(type == "gene"){
tmp <- strsplit(allLines[i], "\\s+|,|;")
if(!is.null(tmp[[1]][1])){
if(tmp[[1]][1] =="NAME"){
name <- tmp[[1]][2]
foundName <- TRUE;
}}
i <- i+1;
}
else if(type == "metabolite"){
tmp <- strsplit(allLines[i], "\\s+|;")
if(!is.null(tmp[[1]][1])){
if(tmp[[1]][1] =="NAME"){
name <- tmp[[1]][2]
foundName <- TRUE;
}}
i <- i+1;
}
}
}
return <- name
}
# trim <- function (x) gsub("^\\s+|\\s+$", "", x)
# getBrites <- function(Associations){
# print("getBrites")
#
# brite<- character();
# # Associations <- Associations[,c(2,5)]
# # Associations <- Associations[!duplicated(Associations),]
# for(j in 1:nrow(Associations)){
#
# url <- getKEGGInfoUrl(Associations[j,3])
#
# foundName <- FALSE;
# allLines <- readLines(url);
# i <- 1;
#
# for(i in 1:length(allLines)){
# temp <- character();
# tmp <- strsplit(allLines[i], "\\s+|;")
# if(!is.null(tmp[[1]][1])){
#
# if(tmp[[1]][1] =="BRITE"){
# foundName <- TRUE;
# if(tmp[[1]][2] == "Compounds"){
# temp <- paste(trim(allLines[i+1]),
# "-", trim(allLines[i+2]),sep = " ");
#
# }else if(tmp[[1]][2] == "Anatomical"){
# temp <-paste(tmp[[1]][2],"-",trim(allLines[i+4]),sep = " ")
# }else if(tmp[[1]][2] == "Pharmaceutical"){
# temp <-paste(tmp[[1]][2],tmp[[1]][3],
# sep = " ")
# }else if(tmp[[1]][2] == "Phytochemical"){
# temp <-paste(tmp[[1]][2],"-",trim(allLines[i+1]),
# sep = " ")
# }else if(tmp[[1]][2] == "Pesticides"){
# temp <-paste(tmp[[1]][2],"-",trim(allLines[i+1]),
# sep = " ")
# }else{
# temp <-paste(tmp[[1]][2],"-",trim(allLines[i+1]), sep = " ")
# }
#
# }
# brite <- append(brite,temp)
# }
#
# }
#
# if(foundName==FALSE){
# temp <- "not classified by KEGG yet"
#
# brite <- append(brite,temp)
# }
#
# }
#
# Associations <- cbind(Associations, "Chemical Class" = as.vector(brite))
# return <- Associations;
# }
getKEGGInfoUrl <- function(keggId){
# print("getKEGGInfoUrl")
url <- "http://rest.kegg.jp/get/"
url <- paste(url, keggId, sep = "")
return <- url;
}
#
# getFirstLevelSubMaps <- function(pathwayId) {
#
# print("getFirstLevelSubMaps")
#
# xmltop <- getKGMLRootNode(pathwayId);
#
#
# mapId <- XML::xpathSApply(xmltop, "//entry[@type = 'map']",
# function(x) (XML::xmlAttrs(x))['name']);
#
# return <- mapId
# }
#
#
#
#
#
#
# isAllGeneOfSubGraphsInKEGGOverview <- function(subGraphId){
#
# print("isAllGeneOfSubGraphsInKEGGOverview")
#
# overviewGeneList <- KEGGREST::keggLink("genes", "hsa01100")
#
#
# subGraphGeneList <- KEGGREST::keggLink("genes", subGraphId)
#
# notInOverview <- c();
# for(i in 1:length(subGraphGeneList)){
#
# subGraphGene_Grep<- paste("\\",subGraphGeneList[[i]],"\\b",sep="")
#
# r <- grep(subGraphGene_Grep, overviewGeneList);
#
# if(length(r) == 0){
# notInOverview <- c(notInOverview,subGraphGeneList[[i]])
# }
#
# }
#
# return(notInOverview)
#
# }
#
# allSubMapsMetaboliteAnalysis <- function(){
#
# print("allSubMapsMetaboliteAnalysis")
#
# allSubMaps <- getFirstLevelSubMaps("hsa01100")
# analysisResults<- NULL;
#
# for(i in 1:length(allSubMaps)){
# allSubMaps[[i]] <- gsub("path:", "", allSubMaps[[i]])
#
# if(substr(allSubMaps[[i]],1,3) == "hsa"){
# mapSubMapId <- gsub("hsa", "map", allSubMaps[[i]])
# numberGeneOfSubMap <- length(KEGGREST::keggLink("cpd",mapSubMapId))
#
# notInOverview <- isAllMetaboliteOfSubGraphsInKEGGOverview(mapSubMapId)
# subMapName <- KEGGREST::keggGet(allSubMaps[[i]])[[1]]$NAME
# subMapClass <- KEGGREST::keggGet(allSubMaps[[i]])[[1]]$CLASS
#
# if(length(notInOverview) == 0){
# notInOverview <- NA;
# numberGeneNotInOverview <- 0;
# }else{
# numberGeneNotInOverview <- length(notInOverview)
# notInOverview <- paste(notInOverview, collapse = ',')
# }
# analysisResults <-rbind(analysisResults,
# c(subMapKEGGId = as.vector(allSubMaps[[i]]),
# subMapName = as.vector(subMapName),
# subMapClass = as.vector(subMapClass),
# numberMetaboliteOfSubMap = as.vector(numberGeneOfSubMap),
# numberMetaboliteNotInOverview = as.vector(numberGeneNotInOverview),
# metaboliteNotInOverviewKEGGId = as.vector(notInOverview)))
#
#
# }
# }
#
# return <- analysisResults;
#
# }
#
# isAllMetaboliteOfSubGraphsInKEGGOverview <- function(subGraphId){
#
# print("isAllMetaboliteOfSubGraphsInKEGGOverview")
#
# overviewMetaboliteList <- KEGGREST::keggLink("cpd", "map01100")
#
#
# subGraphMetaboliteList <- KEGGREST::keggLink("cpd", subGraphId)
#
# notInOverview <- c();
#
# if(length(subGraphMetaboliteList)>0){
# for(i in 1:length(subGraphMetaboliteList)){
#
# subGraphMetabolite_Grep<-
# paste("\\",subGraphMetaboliteList[[i]],"\\b",sep="")
#
# r <- grep(subGraphMetabolite_Grep, overviewMetaboliteList);
#
# if(length(r) == 0){
# notInOverview <- c(notInOverview,subGraphMetaboliteList[[i]])
# }
#
# }
# }
# return(notInOverview)
#
# }
#
# allSubMapsGeneAnalysis <- function(){
#
# print("allSubMapsGeneAnalysis")
#
# allSubMaps <- getFirstLevelSubMaps("hsa01100")
# analysisResults<- NULL;
# for(i in 1:length(allSubMaps)){
# allSubMaps[[i]] <- gsub("path:", "", allSubMaps[[i]])
# if(substr(allSubMaps[[i]],1,3) == "hsa"){
# numberGeneOfSubMap <- length(KEGGREST::keggLink("genes",allSubMaps[[i]]))
#
# notInOverview <- isAllGeneOfSubGraphsInKEGGOverview(allSubMaps[[i]])
# subMapName <- KEGGREST::keggGet(allSubMaps[[i]])[[1]]$NAME
# subMapClass <- KEGGREST::keggGet(allSubMaps[[i]])[[1]]$CLASS
#
# if(length(notInOverview) == 0){
# notInOverview <- NA;
# numberGeneNotInOverview <- 0;
# }else{
# numberGeneNotInOverview <- length(notInOverview)
# notInOverview <- paste(notInOverview, collapse = ',')
# }
# analysisResults <-rbind(analysisResults,
# c(subMapKEGGId = as.vector(allSubMaps[[i]]),
# subMapName = as.vector(subMapName),
# subMapClass = as.vector(subMapClass),
# numberGeneOfSubMap = as.vector(numberGeneOfSubMap),
# numberGeneNotInOverview = as.vector(numberGeneNotInOverview),
# geneNotInOverviewKEGGId = as.vector(notInOverview)))
#
#
#
# }
# }
#
# return <- analysisResults;
#
# }
#
# getHMDBByKEGGId <-function(keggId) {
#
# print("getHMDBByKEGGId")
#
# files <- list.files("./hmdb_metabolites")
# files <- files[-1]
#
# res <- lapply(keggId, function(i)
#
# lapply(files, function(j)
# compareWihtNodeKeggId(j,i)))
#
#
# return <- res;
#
# }
#
# getHMDBInfo <- function(){
#
# print("getHMDBInfo")
#
# files <- list.files("/Users/sandra/Documents/workspaceMetabolomics/hmbdParser/hmdb_metabolites")
# files <- files[-1]
#
# hmdb <- getHMDBIds(files)
#
# kegg_ids <- lapply(files, function(j) getKeggIdByHMDB(j))
# super_class <- lapply(files, function(j) getSuperClassByHMDB(j))
# class <- lapply(files, function(j) getClassByHMDB(j))
# hmdb_infoDF <-data.frame(cbind("hmdb_Id" = as.vector(hmdb),
# "kegg_Id" = as.vector(kegg_ids),
# "super_class" = as.vector(super_class),
# "class" = as.vector(class)))
# exportHMDBInfo(hmdb_infoDF)
# return <- hmdb_infoDF
# }
#
#
# getKeggIdByHMDB <- function(fileName){
#
# print("getKeggIdByHMDB")
#
# fileName <- paste("/Users/sandra/Documents/workspaceMetabolomics/hmbdParser/hmdb_metabolites/", fileName, sep="")
# doc1 <- XML::xmlParse(fileName);
# node_kegg_id <- XML::xpathApply(doc1, "//kegg_id")
#
# kegg_id <- XML::xmlSApply(node_kegg_id, XML::xmlValue)
#
# if(nchar(kegg_id) == 0) kegg_id <- NA;
#
# return <- kegg_id;
# }
#
# getSuperClassByHMDB <- function(fileName){
#
# print("getSuperClassByHMDB")
#
# fileName <- paste("/Users/sandra/Documents/workspaceMetabolomics/hmbdParser/hmdb_metabolites/", fileName, sep="")
# doc1 <- XML::xmlParse(fileName);
#
# node_super_class <- XML::xpathApply(doc1, "//super_class")
#
# super_class <- XML::xmlSApply(node_super_class, XML::xmlValue)
#
# if(nchar(super_class) == 0) super_class <- NA
#
# return <- super_class
# }
#
# getClassByHMDB <- function(fileName){
#
# print("getClassByHMDB")
#
# fileName <- paste("/Users/sandra/Documents/workspaceMetabolomics/hmbdParser/hmdb_metabolites/", fileName, sep="")
# doc1 <- XML::xmlParse(fileName);
#
# node_class <- XML::xpathApply(doc1, "//class")
#
# class <- XML::xmlSApply(node_class, XML::xmlValue)
#
# if(nchar(class) == 0) class <- NA;
#
# return <- class;
# }
#Data <- ldply(files,parse_xml)
#
# getHMDBIds <- function(fileList){
#
# print("getHMDBIds")
# finalList <- lapply(fileList, function(x) gsub( ".xml", "",x))
# return <- finalList;
#
# }
#
# exportHMDBInfo <- function(hmdb_infoDF){
#
# print("exportHMDBInfo")
# hmdb_infoDF <- data.frame(lapply(hmdb_infoDF, as.character), stringsAsFactors=FALSE)
# exportDFtoTxt(hmdb_infoDF, "hmdb_info")
# }
#
#
# getHMDBIdByKEggId <- function(keggIdList){
#
# print("getHMDBIdByKEggId")
#
# res <- importTXTtoDF("hmdb_info.txt")
#
# r <-lapply(keggIdList, function(x) subset(res, res[2] == x));
#
# r <- do.call(rbind, r)
#
# r <- prepOutputHMDBIdByKEggId(r);
#
# return <- r[,c(2,1)];
# }
## could also annotate from HMDB database
getSuperClassByKEggId <- function(kegg.id.list){
# print("getSuperClassByKEggId")
# retrieve data from HMDB xml files
hmdb.data <- data.frame(importTXTtoDF("hmdb_info.txt"))
# hmdb.data <- load("")
# print(typeof(hmdb.data))
# print(hmdb.data)
# unlist the data to for lapply
kegg.id.list <- unlist(kegg.id.list)
# print(kegg.id.list)
r <- lapply(kegg.id.list, function(x) {
x.1 <- paste("\\b", x,"\\b",sep="")
if (nrow(hmdb.data[grep(x.1, hmdb.data$kegg_Id),]) == 0) {
data.frame("hmdb_Id" = NA,
"kegg_Id" = x,
"super_class" = NA,
"class" = NA)
# carefull I only took the first line
# but multiple line mean multiple classes that should be
# bind together
} else {
hmdb.data[grep(x.1, hmdb.data$kegg_Id),][1,]
}
});
#bind the results for each compound
r <- do.call(rbind, r)
return <- r[,3];
}
#
# getClassByKEggId <- function(keggIdList){
#
# print("getClassByKEggId")
#
# res <- importTXTtoDF("hmdb_info.txt")
#
# r <-lapply(keggIdList, function(x) subset(res, res[2] == x));
#
# r <- do.call(rbind, r)
#
# # r <- prepOutputHMDBIdByKEggId(r);
#
# return <- r[,c(2,4)];
# }
#
# getAllHMDBbyKeggId <- function(keggIdList){
#
# print("getAllHMDBbyKeggId")
#
# res <- importTXTtoDF("hmdb_info.txt")
#
# r <-lapply(keggIdList, function(x) subset(res, res[2] == x));
#
# r <- do.call(rbind, r)
#
# # r <- prepOutputHMDBIdByKEggId(r);
#
# return <- r;
# }
#
# ## put this in a general data frame help function
# prepOutputHMDBIdByKEggId <- function(metabolitesNamesDF){
#
# print("prepOutputHMDBIdByKEggId")
#
# metabo <- ""
# hmdb_ids <- ""
# df <- data.frame();
#
# for(x in 1:nrow(metabolitesNamesDF)){
# # conditino to get first row
# if(metabo == ""){
# metabo <- metabolitesNamesDF[x,2];
# hmdb_ids <- paste(hmdb_ids, metabolitesNamesDF[x,1])
#
# # conditino get inside rows and combine first colinfo info based on
# # duplicated 2 col
# }else if(!(metabo == as.character(metabolitesNamesDF[x,2]))){
#
# df <- rbind(df, data.frame("keggId" = as.vector(as.character(metabo)),
# "hmdbIds" = as.vector(hmdb_ids)))
# hmdb_ids <- "";
# metabo <- metabolitesNamesDF[x,2]
# hmdb_ids <- paste(hmdb_ids, metabolitesNamesDF[x,1])
#
# }else{
# hmdb_ids <- paste(hmdb_ids, metabolitesNamesDF[x,1])
# }
#
# # ctach last row
# if(x == nrow(metabolitesNamesDF)){
# df <- rbind(df, data.frame("keggId" = as.vector(as.character(metabo)),
# "hmdbIds" = as.vector(hmdb_ids)))
# }
# }
#
#
# return <- df;
#
# }
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