getKO<-function(marker){ require(XML) url<-paste("http://www.genome.jp/dbget-bin/www_bget?cpd:",marker,sep="") table<-readHTMLTable(url) ko<-table[6][[1]]$V1 return(ko) } trans<-function(x){paste(unlist(x), sep=",", collapse=",")} PushToBox<-function(detain){ for ( i in which(sapply(detain,is.

list ))){ detain[i]<-apply(detain[i], 1, trans) } return(detain) } ProvideKO<-function(t){ require(XML) url<-paste("http://www.genome.jp/dbget-bin/www_bget?cpd:",t[num],sep="") table<-readHTMLTable(url) ko<-as.character(table[6][[1]]$V1) return(ko) } ProvidePathway<-function(t){ require(XML) url<-paste("http://www.genome.jp/dbget-bin/www_bget?cpd:",t[num],sep="") table<-readHTMLTable(url) pathway<-as.character(table[6][[1]]$V2) return(pathway) } MapingToKEGGpathway<-function(path=getwd(), files=NULL, Cname=NULL, format,heade r=TRUE){ if (is.null(files)) { if (format == "csv") { if (length(grep("csv", dir(path))) == 0){ stop("there are not csv files in the provided path ..") } else{ ii<-grep("csv", dir(path)) detain=NULL for (i in ii){ filedata<-read.csv(dir(path)[i]) detain<-rbind(detain, filedata) } } } if (format=="xlsx"){ require(gdata) if(length(grep("xlsx", dir(path)))!=0){ detain=NULL for (i in grep("xlsx",dir(path))){ filedata<-read.xls(dir(path)[i], sheet=1)

detain=rbind(detain, filedata) } } } }else{ filenames<-files detain=NULL for (filename in filenames) { if(format=="csv"){ filedata = read.csv(filename,header = header) detain=rbind(detain,filedata) } if(format=="xlsx"){ require(gdata) filedata=read.xls(filename,sheet=1) } } } if(mode(Cname)=="numeric"){ num<<-Cname } if((Cname)=="character"){ num<<-grep(Cname, colnames(detain)) } message("Linking to KEGG...") KO<-apply(detain, 1, ProvideKO) Pathway<-apply(detain,1,ProvidePathway) message("End ") # detain$KO<-as.character(I(KO)) # detain$Pathway<-as.character(I(Pathway)) detain$KO<-KO detain$Pathway<-Pathway detain<-PushToBox(detain) return(detain) } ################################################################################ ## re<-MapingToKEGGpathway(path=getwd(),files=NULL,Cname=11, format="csv") #write.table(re, "xiongjieKEGG_output.txt", quote=F, row.names=F, sep="\t")