Nothing
R/Annotations.R
In FunCluster: Functional Profiling of Microarray Expression Data
Defines functions
ChargerKegg
GeneInfo
GeneInfoSC
MakeLocusNames
Documented in
ChargerKegg
GeneInfo
GeneInfoSC
MakeLocusNames
.packageName <- "FunCluster"
MiseEnFormeKegg <- function ( ligne, Fichier) {
vec1 <- ligne
LL <-as.character( vec1[1])
if (!identical(all.equal( as.numeric(LL), as.numeric(NA)),TRUE) ){
Kmap <- as.character(vec1[-1])
Kmap <- Kmap [ Kmap != ""]
NbKmap <- length (Kmap)
LocusLink <- gl ( 1, NbKmap, label = LL)
LLcorrespondance <- cbind.data.frame( LocusLink, Kmap )
write.table ( LLcorrespondance, Fichier ,col.names =FALSE,row.names=FALSE,append = TRUE, sep= "\t",quote = FALSE)
}
}
MiseEnFormeKeggSC <- function ( ligne, Fichier) {
vec1 <- ligne
LL <-as.character( vec1[1])
Kmap <- as.character(vec1[-1])
Kmap <- Kmap [ Kmap != ""]
NbKmap <- length (Kmap)
LocusLink <- gl ( 1, NbKmap, label = LL)
LLcorrespondance <- cbind.data.frame( LocusLink, Kmap )
write.table ( LLcorrespondance, Fichier ,col.names =FALSE,row.names=FALSE,append = TRUE, sep= "\t",quote = FALSE)
}
ChargerKegg <- function(espece = espece) {
if ( espece == "hsa" ) {
DIResp <- "HS"
} else {
if ( espece == "mmu"){
DIResp <- "MM"
}else if(espece == "sce"){
DIResp <- "SC"
}
}
download.file ( paste("ftp://ftp.genome.ad.jp/pub/kegg/pathway/organisms/",espece,"/",espece,"_gene_map.tab",sep="") , paste(getwd(),"/Annotations/KEGG/",DIResp,"/tmp.txt",sep=""), mode = "w" )
FichierFinalNonQuote <- file (paste(getwd(),"/Annotations/KEGG/",DIResp,"/ll_keggNonQuote.txt",sep=""), "w+")
FichierFinal <- file (paste(getwd(),"/Annotations/KEGG/",DIResp,"/ll_kegg.txt",sep=""), "w")
tempo <- file (paste(getwd(),"/Annotations/KEGG/",DIResp,"/tmp.txt",sep=""), "r")
tempo2 <- file (paste(getwd(),"/Annotations/KEGG/",DIResp,"/tmp2.txt",sep=""), "w+")
NbCol <- count.fields(file=tempo)
MaxNbCol <- max (NbCol)
seek ( tempo, where = 0)
DTtemp <- read.table ( file = tempo ,na.strings = "",fill=TRUE,colClasses="character",sep= "\t",header = FALSE,quote = "",comment.char = "")
write.table ( DTtemp, tempo2 ,col.names =FALSE,row.names=FALSE,quote =FALSE, sep = "\t")
DTtemp <- read.table ( file = tempo2 ,fill=TRUE,colClasses="character",col.names =c(1: (MaxNbCol)),sep= "", quote = "",comment.char = "")
close(tempo)
close(tempo2)
unlink(paste(getwd(),"/Annotations/KEGG/",DIResp,"/tmp.txt",sep=""))
unlink (paste(getwd(),"/Annotations/KEGG/",DIResp,"/tmp2.txt",sep=""))
if(espece == "hsa" || espece == "mmu"){
suppressWarnings (apply (DTtemp, 1, FUN = "MiseEnFormeKegg" ,FichierFinalNonQuote))
}else if (espece == "sce"){
suppressWarnings (apply (DTtemp, 1, FUN = "MiseEnFormeKeggSC" ,FichierFinalNonQuote))
}
if ( espece == "hsa" ) {
HS.KEGG.file.annot <<- read.table ( file = FichierFinalNonQuote ,na.strings = "",fill=TRUE,colClasses="character",sep= "\t",header = FALSE,quote = "",comment.char = "")
write.table (HS.KEGG.file.annot , FichierFinal ,col.names =FALSE,row.names=FALSE,append = TRUE, sep= "\t")
} else if ( espece == "mmu"){
MM.KEGG.file.annot <<- read.table ( file = FichierFinalNonQuote ,na.strings = "",fill=TRUE,colClasses="character",sep= "\t",header = FALSE,quote = "",comment.char = "")
write.table (MM.KEGG.file.annot , FichierFinal ,col.names =FALSE,row.names=FALSE,append = TRUE, sep= "\t")
}else if(espece == "sce"){
SC.KEGG.file.annot <<- read.table ( file = FichierFinalNonQuote ,na.strings = "",fill=TRUE,colClasses="character",sep= "\t",header = FALSE,quote = "",comment.char = "")
DTLL <- GeneInfoSC()
DTLL <- as.matrix(DTLL[DTLL[,1] == "4932",])
rownames(DTLL) <- as.character(DTLL[,4])
SC.KEGG.file.annot <<- as.matrix(SC.KEGG.file.annot)
rownames(SC.KEGG.file.annot) <<- as.character(SC.KEGG.file.annot[,1])
x <- DTLL[DTLL[,4] %in% as.character(SC.KEGG.file.annot[,1]),2]
SC.KEGG.file.annot <<- SC.KEGG.file.annot[SC.KEGG.file.annot[,1] %in% names(x),]
y <- NULL
for(i in 1:nrow(SC.KEGG.file.annot)){
y <- rbind(y,c(x[SC.KEGG.file.annot[i,1]],SC.KEGG.file.annot[i,2]))
}
colnames(y) <- as.character(matrix("",1,ncol(y)))
SC.KEGG.file.annot <<- y
write.table (SC.KEGG.file.annot , FichierFinal ,col.names =FALSE, row.names=FALSE,append = TRUE, sep= "\t")
}
close (FichierFinalNonQuote)
unlink(paste(getwd(),"/Annotations/KEGG/",DIResp,"/ll_keggNonQuote.txt",sep=""))
close (FichierFinal)
}
Kegg <- function () {
dir.create(paste(getwd(),"/Annotations/KEGG",sep=""))
download.file ( "ftp://ftp.genome.ad.jp/pub/kegg/pathway/map_title.tab" ,paste(getwd(), "/Annotations/KEGG/Temp_kegg_terms.txt",sep=""), mode = "w" )
temp <- file (paste(getwd(),"/Annotations/KEGG/Temp_kegg_terms.txt",sep=""),"r")
Fichkeggterms <- file (paste(getwd(),"/Annotations/KEGG/kegg_terms.txt",sep=""),"w")
KEGG.terms.name <<- read.table (file = temp ,na.strings = "",fill=TRUE,colClasses="character",sep= "\t",header = FALSE,quote = "",comment.char = "")
write.table ( KEGG.terms.name, Fichkeggterms ,col.names =FALSE,row.names=FALSE, sep = "\t")
close (temp)
close (Fichkeggterms)
unlink ( paste(getwd(),"/Annotations/KEGG/Temp_kegg_terms.txt",sep=""))
dir.create (paste(getwd(),"/Annotations/KEGG/HS",sep=""))
ChargerKegg ("hsa")
dir.create (paste(getwd(),"/Annotations/KEGG/MM",sep=""))
ChargerKegg ("mmu")
dir.create (paste(getwd(),"/Annotations/KEGG/SC",sep=""))
ChargerKegg ("sce")
}
MakeGoTerms <- function (DTGoTermsAndIds) {
DTGoTermsAndIds <- DTGoTermsAndIds [ substr ( DTGoTermsAndIds[,1],1,1) != "!" ,]
dimens <- nrow(DTGoTermsAndIds)
DTGoTermsAndIds <- cbind.data.frame( DTGoTermsAndIds, row.names = c(1: dimens))
GO.terms.name <<- DTGoTermsAndIds [,1:2]
FichierFinal <- file (paste(getwd(),"/Annotations/GO/go_terms.txt",sep=""), "w")
write.table ( GO.terms.name , FichierFinal ,col.names =FALSE,row.names=FALSE, sep = "\t")
close ( FichierFinal )
}
MakeGoHierarchy <- function (DATE="") {
if(DATE == ""){
DATE <- Sys.time()
DATE <- substr( as.character(DATE),1,7)
DATE <- gsub("-","",DATE)
}
NomFichier <- paste ( "go_", DATE , "-termdb-tables.tar.gz" ,sep = "")
download.file(paste ("http://godatabase-archive.stanford.edu/latest/", NomFichier,sep = ""),paste (getwd(),"/go_DATE-termdb-tables.tar.gz",sep=""),mode="wb")
system("gunzip go_DATE-termdb-tables.tar.gz")
system("tar -xf go_DATE-termdb-tables.tar")
FichTerm2term <- file (paste(getwd(),"/go_",DATE,"-termdb-tables/term2term.txt",sep=""), "r")
FichTerm <- file (paste(getwd(),"/go_",DATE,"-termdb-tables/term.txt",sep=""), "r")
FichFinal <- file (paste(getwd(),"/Annotations/GO/go_hierarchy.txt",sep=""), "w")
DTterm2term <- read.table ( file = FichTerm2term ,na.strings = "",fill=TRUE,colClasses="character",col.names =c(1:5),sep= "\t",header = FALSE, quote = "",comment.char = "")
DTterm <- read.table ( file = FichTerm ,na.strings = "",fill=TRUE,colClasses="character",col.names =c(1:6),sep= "\t",header = FALSE, quote = "",comment.char = "")
GO.terms.hierarchy <<- cbind ( DTterm [ DTterm2term[,4],4],DTterm [ DTterm2term[,3],4] )
write.table ( GO.terms.hierarchy, FichFinal ,col.names =FALSE,row.names=FALSE, sep= "\t")
close ( FichTerm2term )
close(FichTerm )
close (FichFinal)
unlink (paste (getwd(),"/go_DATE-termdb-tables.tar",sep=""))
unlink (paste(getwd(),"/go_",DATE,"-termdb-tables",sep=""), recursive = TRUE)
return (GO.terms.hierarchy)
}
AnnotationIndirecte <- function (DTGOOntology,DTGOHierarchy , DIResp, NomFichFinal ) {
FichFinal <- file (paste(getwd(),"/Annotations/GO/",DIResp,"/IND/",NomFichFinal,".txt",sep= ""), "w")
DTIND <- merge ( DTGOOntology, DTGOHierarchy , by.x= 2,by.y = 1)
names(DTIND)<-c("X0",names(DTGOOntology))
DTIND <- rbind.data.frame ( DTGOOntology, DTIND[,2:3] )
OrdreLignes <- do.call("order", DTIND[,c( 1,2)])
DTIND <- DTIND [ OrdreLignes,]
DTIND <- unique.data.frame (DTIND)
dimens <- nrow(DTIND)
DTIND <- cbind.data.frame( DTIND, row.names = c(1: dimens))
write.table ( DTIND, FichFinal ,col.names =FALSE,row.names=FALSE,sep="\t")
close( FichFinal )
return (DTIND)
}
TroisiemeFiltrage <- function (DTGoTermsAndIds,DTLoc2GoFiltre1, FichOntology ,initialeOntology) {
OntDTGoTermsAndIds <- DTGoTermsAndIds[ DTGoTermsAndIds[,3] == initialeOntology,]
DTOntology <- DTLoc2GoFiltre1 [ DTLoc2GoFiltre1[,2] %in% OntDTGoTermsAndIds[,1],]
DTOntology <- unique.data.frame (DTOntology)
OrdreLignes <- do.call("order", DTOntology[,c( 1,2)])
DTOntology <- DTOntology [ OrdreLignes,]
dimens <- nrow(DTOntology)
DTOntology <- cbind.data.frame( DTOntology, row.names = c(1: dimens))
write.table ( DTOntology, FichOntology ,col.names =FALSE,row.names=FALSE,sep="\t")
return (DTOntology)
}
GeneInfo <- function(){
download.file ( paste("ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz",sep="") ,paste( getwd(),"/Annotations/Temp.gz",sep=""), mode = "wb" )
LLTempgz <- gzfile (paste(getwd(),"/Annotations/Temp.gz",sep=""),"rb")
LLTemp <- file (paste(getwd(),"/Annotations/Temp.txt",sep=""), "w+")
vecTemp <- readLines(LLTempgz)
cat ( vecTemp , file = LLTemp, sep = "\n")
rm(vecTemp)
DTLLbrut <- read.table ( file = LLTemp,na.strings = "-",fill=TRUE,colClasses="character",sep= "\t",header = FALSE, quote = "",comment.char = "#")
DTLL <- cbind(DTLLbrut[,1],DTLLbrut[,2],DTLLbrut[,7],DTLLbrut[,8],DTLLbrut[,9])
close(LLTempgz)
close (LLTemp)
unlink (paste(getwd(),"/Annotations/Temp.gz",sep=""))
unlink (paste(getwd(),"/Annotations/Temp.txt",sep=""))
return (DTLL)
}
GeneInfoSC <- function(){
download.file ( paste("ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz",sep="") ,paste( getwd(),"/Annotations/Temp.gz",sep=""), mode = "wb" )
LLTempgz <- gzfile (paste(getwd(),"/Annotations/Temp.gz",sep=""),"rb")
LLTemp <- file (paste(getwd(),"/Annotations/Temp.txt",sep=""), "w+")
vecTemp <- readLines(LLTempgz)
cat ( vecTemp , file = LLTemp, sep = "\n")
rm(vecTemp)
DTLLbrut <- read.table ( file = LLTemp,na.strings = "-",fill=TRUE ,colClasses="character",sep= "\t",header = FALSE, quote = "",comment.char = "#")
DTLL <- cbind(DTLLbrut[,1],DTLLbrut[,2],DTLLbrut[,3],DTLLbrut[,4],DTLLbrut[,7],DTLLbrut[,8],DTLLbrut[,9])
close(LLTempgz)
close (LLTemp)
unlink (paste(getwd(),"/Annotations/Temp.gz",sep=""))
unlink (paste(getwd(),"/Annotations/Temp.txt",sep=""))
return (DTLL)
}
MakeCorrespondanceLLGO <- function (DTLoc2Go, DTGoTermsAndIds,DTGOHierarchy, espece = espece) {
if ( espece == "hs" ) {
DIResp <- "HS"
DTLoc2Go <- DTLoc2Go[DTLoc2Go[,1] == "9606",2:3]
} else {
if ( espece == "mm"){
DIResp <- "MM"
DTLoc2Go <- DTLoc2Go[DTLoc2Go[,1] == "10090",2:3]
}else if (espece == "sc"){
DIResp <- "SC"
DTLoc2Go <- DTLoc2Go[DTLoc2Go[,1] == "4932",2:3]
}
}
FichBioProcess <- file (paste(getwd(),"/Annotations/GO/",DIResp,"/DIR/biological_process.txt",sep= ""), "w")
FichCellComp <- file (paste(getwd(),"/Annotations/GO/",DIResp,"/DIR/cellular_component.txt",sep= ""), "w")
FichMolFunc <- file (paste(getwd(),"/Annotations/GO/",DIResp,"/DIR/molecular_function.txt",sep= ""), "w")
DTLoc2GoFiltre1 <- DTLoc2Go[ DTLoc2Go[,2] %in% DTGoTermsAndIds[,1],1:2]
if ( espece == "hs" ) {
HS.GO.DIR.BP.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichBioProcess ,"P")
HS.GO.DIR.CC.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichCellComp ,"C")
HS.GO.DIR.MF.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichMolFunc ,"F")
HS.GO.IND.BP.file.annot <<- AnnotationIndirecte (HS.GO.DIR.BP.file.annot,DTGOHierarchy,DIResp,"biological_process")
HS.GO.IND.CC.file.annot <<- AnnotationIndirecte (HS.GO.DIR.CC.file.annot,DTGOHierarchy,DIResp,"cellular_component")
HS.GO.IND.MF.file.annot <<- AnnotationIndirecte (HS.GO.DIR.MF.file.annot,DTGOHierarchy,DIResp,"molecular_function")
} else {
if ( espece == "mm"){
MM.GO.DIR.BP.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichBioProcess ,"P")
MM.GO.DIR.CC.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichCellComp ,"C")
MM.GO.DIR.MF.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichMolFunc ,"F")
MM.GO.IND.BP.file.annot <<- AnnotationIndirecte (MM.GO.DIR.BP.file.annot,DTGOHierarchy,DIResp,"biological_process")
MM.GO.IND.CC.file.annot <<- AnnotationIndirecte (MM.GO.DIR.CC.file.annot,DTGOHierarchy,DIResp,"cellular_component")
MM.GO.IND.MF.file.annot <<- AnnotationIndirecte (MM.GO.DIR.MF.file.annot,DTGOHierarchy,DIResp,"molecular_function")
}else if(espece == "sc"){
SC.GO.DIR.BP.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichBioProcess ,"P")
SC.GO.DIR.CC.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichCellComp ,"C")
SC.GO.DIR.MF.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichMolFunc ,"F")
SC.GO.IND.BP.file.annot <<- AnnotationIndirecte (SC.GO.DIR.BP.file.annot,DTGOHierarchy,DIResp,"biological_process")
SC.GO.IND.CC.file.annot <<- AnnotationIndirecte (SC.GO.DIR.CC.file.annot,DTGOHierarchy,DIResp,"cellular_component")
SC.GO.IND.MF.file.annot <<- AnnotationIndirecte (SC.GO.DIR.MF.file.annot,DTGOHierarchy,DIResp,"molecular_function")
}
}
close(FichBioProcess)
close(FichCellComp)
close (FichMolFunc)
}
MakeLocusNames <- function( espece, DTLL ) {
if ( espece == "hs" ) {
DTLLesp <- DTLL[DTLL[,1] == "9606",2:5]
DIResp <- "HS"
} else {
if ( espece == "mm"){
DTLLesp <- DTLL[DTLL[,1] == "10090",2:5]
DIResp <- "MM"
}else if(espece == "sc"){
DTLLesp <- DTLL[DTLL[,1] == "4932",2:5]
DIResp <- "SC"
}
}
DTLLloc <- DTLLesp[, c(1,2,3)]
DTLLloc <- unique.data.frame (DTLLloc)
dimens <- nrow(DTLLloc)
DTLLloc <- cbind.data.frame( DTLLloc, row.names = c(1: dimens)) #
DTLLloc <- DTLLloc[2:nrow(DTLLloc),]
FichierLocation <- file (paste(getwd(),"/Annotations/LL/",DIResp,"/location.txt",sep= ""), "w")
write.table ( DTLLloc, FichierLocation ,col.names =FALSE,row.names=FALSE, sep="\t")
DTLLesp <- DTLLesp[, c(1,4)]
DTLLesp <- unique.data.frame (DTLLesp)
dimens <- nrow(DTLLesp)
DTLLesp <- cbind.data.frame( DTLLesp, row.names = c(1: dimens))
DTLLesp <- DTLLesp[2:nrow(DTLLesp),]
FichierFinal <- file (paste(getwd(),"/Annotations/LL/",DIResp,"/locus_name.txt",sep= ""), "w")
write.table ( DTLLesp, FichierFinal ,col.names =FALSE,row.names=FALSE, sep="\t")
if ( espece == "hs" ) {
HS.locus.name <<- DTLLesp
HS.locus.cyto <<- DTLLloc
} else {
if ( espece == "mm"){
MM.locus.name <<- DTLLesp
MM.locus.cyto <<- DTLLloc
}else if(espece == "sc"){
SC.locus.name <<- DTLLesp
SC.locus.cyto <<- DTLLloc
}
}
close ( FichierFinal )
close(FichierLocation)
}
goAndLL <- function (DATE="") {
dir.create (paste(getwd(),"/Annotations/GO",sep=""))
download.file ( "http://www.geneontology.org/doc/GO.terms_and_ids" ,paste(getwd(),"/Annotations/GO/GoTermsTmp.txt",sep=""), mode = "w" )
FichGoTermsAndIds <- file (paste(getwd(),"/Annotations/GO/GoTermsTmp.txt",sep=""), "r")
DTGoTermsAndIds <- read.table ( file = FichGoTermsAndIds ,na.strings = "",fill=TRUE,colClasses="character",col.names =c(1:3),sep= "\t",header = FALSE, quote = "",comment.char = "")
close(FichGoTermsAndIds)
unlink(paste(getwd(),"/Annotations/GO/GoTermsTmp.txt",sep=""))
download.file ( "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz" ,paste(getwd(),"/Annotations/GO/gene2go.gz",sep=""), mode = "wb" )
Gene2GOTempgz <- gzfile (paste(getwd(),"/Annotations/GO/gene2go.gz",sep=""),"rb")
Gene2GOTemp <- file (paste(getwd(),"/Annotations/GO/gene2go.txt",sep=""), "w+")
vecTemp <- readLines(Gene2GOTempgz)
cat ( vecTemp , file = Gene2GOTemp, sep = "\n")
DTLoc2Go <- read.table ( file = Gene2GOTemp,na.strings = "",fill=TRUE ,colClasses="character",col.names =c(1:8),sep= "\t",header = FALSE, quote = "",comment.char = "#")
close (Gene2GOTemp)
unlink(paste(getwd(),"/Annotations/GO/gene2go.txt",sep=""))
close (Gene2GOTempgz)
unlink(paste(getwd(),"/Annotations/GO/gene2go.gz",sep=""))
MakeGoTerms (DTGoTermsAndIds)
DTGoHierarchy <- MakeGoHierarchy (DATE=DATE)
DTLL <- GeneInfo()
dir.create (paste(getwd(),"/Annotations/GO/HS",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/HS/DIR",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/HS/IND",sep=""))
MakeCorrespondanceLLGO (DTLoc2Go,DTGoTermsAndIds, DTGoHierarchy , "hs")
dir.create (paste(getwd(),"/Annotations/GO/MM",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/MM/DIR",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/MM/IND",sep=""))
MakeCorrespondanceLLGO (DTLoc2Go, DTGoTermsAndIds, DTGoHierarchy , "mm")
dir.create (paste(getwd(),"/Annotations/GO/SC",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/SC/DIR",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/SC/IND",sep=""))
MakeCorrespondanceLLGO (DTLoc2Go, DTGoTermsAndIds, DTGoHierarchy , "sc")
dir.create(paste(getwd(),"/Annotations/LL",sep=""))
dir.create (paste(getwd(),"/Annotations/LL/HS",sep=""))
MakeLocusNames ( "hs", DTLL)
dir.create (paste(getwd(),"/Annotations/LL/MM",sep=""))
MakeLocusNames ( "mm", DTLL)
dir.create (paste(getwd(),"/Annotations/LL/SC",sep=""))
MakeLocusNames ( "sc", DTLL)
}
annotations <- function (date.annot="") {
dir.create (paste (getwd(),"/Annotations", sep= ""))
Kegg ()
goAndLL(DATE=date.annot)
annot.date <- format(Sys.time(), "%Y %b %d")
# GO.terms.hierarchy <-GO.terms.hierarchy[(GO.terms.hierarchy[,1] %in% GO.terms.name[,1]) && (GO.terms.hierarchy[,2] %in% GO.terms.name[,1]),]
#
# HS.GO.DIR.BP.file.annot <- HS.GO.DIR.BP.file.annot[(HS.GO.DIR.BP.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.DIR.BP.file.annot[,1] %in% HS.locus.name[,1]),]
# HS.GO.DIR.CC.file.annot <- HS.GO.DIR.CC.file.annot[(HS.GO.DIR.CC.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.DIR.CC.file.annot[,1] %in% HS.locus.name[,1]),]
# HS.GO.DIR.MF.file.annot <- HS.GO.DIR.MF.file.annot[(HS.GO.DIR.MF.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.DIR.MF.file.annot[,1] %in% HS.locus.name[,1]),]
# HS.GO.IND.BP.file.annot <- HS.GO.IND.BP.file.annot[(HS.GO.IND.BP.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.IND.BP.file.annot[,1] %in% HS.locus.name[,1]),]
# HS.GO.IND.CC.file.annot <- HS.GO.IND.CC.file.annot[(HS.GO.IND.CC.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.IND.CC.file.annot[,1] %in% HS.locus.name[,1]),]
# HS.GO.IND.MF.file.annot <- HS.GO.IND.MF.file.annot[(HS.GO.IND.MF.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.IND.MF.file.annot[,1] %in% HS.locus.name[,1]),]
#
# MM.GO.DIR.BP.file.annot <- MM.GO.DIR.BP.file.annot[(MM.GO.DIR.BP.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.DIR.BP.file.annot[,1] %in% MM.locus.name[,1]),]
# MM.GO.DIR.CC.file.annot <- MM.GO.DIR.CC.file.annot[(MM.GO.DIR.CC.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.DIR.CC.file.annot[,1] %in% MM.locus.name[,1]),]
# MM.GO.DIR.MF.file.annot <- MM.GO.DIR.MF.file.annot[(MM.GO.DIR.MF.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.DIR.MF.file.annot[,1] %in% MM.locus.name[,1]),]
# MM.GO.IND.BP.file.annot <- MM.GO.IND.BP.file.annot[(MM.GO.IND.BP.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.IND.BP.file.annot[,1] %in% MM.locus.name[,1]),]
# MM.GO.IND.CC.file.annot <- MM.GO.IND.CC.file.annot[(MM.GO.IND.CC.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.IND.CC.file.annot[,1] %in% MM.locus.name[,1]),]
# MM.GO.IND.MF.file.annot <- MM.GO.IND.MF.file.annot[(MM.GO.IND.MF.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.IND.MF.file.annot[,1] %in% MM.locus.name[,1]),]
#
# SC.GO.DIR.BP.file.annot <- SC.GO.DIR.BP.file.annot[(SC.GO.DIR.BP.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.DIR.BP.file.annot[,1] %in% SC.locus.name[,1]),]
# SC.GO.DIR.CC.file.annot <- SC.GO.DIR.CC.file.annot[(SC.GO.DIR.CC.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.DIR.CC.file.annot[,1] %in% SC.locus.name[,1]),]
# SC.GO.DIR.MF.file.annot <- SC.GO.DIR.MF.file.annot[(SC.GO.DIR.MF.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.DIR.MF.file.annot[,1] %in% SC.locus.name[,1]),]
# SC.GO.IND.BP.file.annot <- SC.GO.IND.BP.file.annot[(SC.GO.IND.BP.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.IND.BP.file.annot[,1] %in% SC.locus.name[,1]),]
# SC.GO.IND.CC.file.annot <- SC.GO.IND.CC.file.annot[(SC.GO.IND.CC.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.IND.CC.file.annot[,1] %in% SC.locus.name[,1]),]
# SC.GO.IND.MF.file.annot <- SC.GO.IND.MF.file.annot[(SC.GO.IND.MF.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.IND.MF.file.annot[,1] %in% SC.locus.name[,1]),]
save(GO.terms.hierarchy,GO.terms.name,HS.GO.DIR.BP.file.annot,HS.GO.DIR.CC.file.annot,HS.GO.DIR.MF.file.annot,
HS.GO.IND.BP.file.annot,HS.GO.IND.CC.file.annot,HS.GO.IND.MF.file.annot,HS.KEGG.file.annot,HS.locus.name,HS.locus.cyto,KEGG.terms.name,
MM.GO.DIR.BP.file.annot,MM.GO.DIR.CC.file.annot,MM.GO.DIR.MF.file.annot,MM.GO.IND.BP.file.annot,MM.GO.IND.CC.file.annot,
MM.GO.IND.MF.file.annot,MM.KEGG.file.annot,MM.locus.name,MM.locus.cyto,SC.GO.DIR.BP.file.annot,SC.GO.DIR.CC.file.annot,SC.GO.DIR.MF.file.annot,
SC.GO.IND.BP.file.annot,SC.GO.IND.CC.file.annot,SC.GO.IND.MF.file.annot,SC.KEGG.file.annot,SC.locus.name,SC.locus.cyto,
annot.date,file="sysdata.rda",compress=TRUE)
q(save="no")
}
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Defines functions ChargerKegg GeneInfo GeneInfoSC MakeLocusNames
Documented in ChargerKegg GeneInfo GeneInfoSC MakeLocusNames
.packageName <- "FunCluster"
MiseEnFormeKegg <- function ( ligne, Fichier) {
vec1 <- ligne
LL <-as.character( vec1[1])
if (!identical(all.equal( as.numeric(LL), as.numeric(NA)),TRUE) ){
Kmap <- as.character(vec1[-1])
Kmap <- Kmap [ Kmap != ""]
NbKmap <- length (Kmap)
LocusLink <- gl ( 1, NbKmap, label = LL)
LLcorrespondance <- cbind.data.frame( LocusLink, Kmap )
write.table ( LLcorrespondance, Fichier ,col.names =FALSE,row.names=FALSE,append = TRUE, sep= "\t",quote = FALSE)
}
}
MiseEnFormeKeggSC <- function ( ligne, Fichier) {
vec1 <- ligne
LL <-as.character( vec1[1])
Kmap <- as.character(vec1[-1])
Kmap <- Kmap [ Kmap != ""]
NbKmap <- length (Kmap)
LocusLink <- gl ( 1, NbKmap, label = LL)
LLcorrespondance <- cbind.data.frame( LocusLink, Kmap )
write.table ( LLcorrespondance, Fichier ,col.names =FALSE,row.names=FALSE,append = TRUE, sep= "\t",quote = FALSE)
}
ChargerKegg <- function(espece = espece) {
if ( espece == "hsa" ) {
DIResp <- "HS"
} else {
if ( espece == "mmu"){
DIResp <- "MM"
}else if(espece == "sce"){
DIResp <- "SC"
}
}
download.file ( paste("ftp://ftp.genome.ad.jp/pub/kegg/pathway/organisms/",espece,"/",espece,"_gene_map.tab",sep="") , paste(getwd(),"/Annotations/KEGG/",DIResp,"/tmp.txt",sep=""), mode = "w" )
FichierFinalNonQuote <- file (paste(getwd(),"/Annotations/KEGG/",DIResp,"/ll_keggNonQuote.txt",sep=""), "w+")
FichierFinal <- file (paste(getwd(),"/Annotations/KEGG/",DIResp,"/ll_kegg.txt",sep=""), "w")
tempo <- file (paste(getwd(),"/Annotations/KEGG/",DIResp,"/tmp.txt",sep=""), "r")
tempo2 <- file (paste(getwd(),"/Annotations/KEGG/",DIResp,"/tmp2.txt",sep=""), "w+")
NbCol <- count.fields(file=tempo)
MaxNbCol <- max (NbCol)
seek ( tempo, where = 0)
DTtemp <- read.table ( file = tempo ,na.strings = "",fill=TRUE,colClasses="character",sep= "\t",header = FALSE,quote = "",comment.char = "")
write.table ( DTtemp, tempo2 ,col.names =FALSE,row.names=FALSE,quote =FALSE, sep = "\t")
DTtemp <- read.table ( file = tempo2 ,fill=TRUE,colClasses="character",col.names =c(1: (MaxNbCol)),sep= "", quote = "",comment.char = "")
close(tempo)
close(tempo2)
unlink(paste(getwd(),"/Annotations/KEGG/",DIResp,"/tmp.txt",sep=""))
unlink (paste(getwd(),"/Annotations/KEGG/",DIResp,"/tmp2.txt",sep=""))
if(espece == "hsa" || espece == "mmu"){
suppressWarnings (apply (DTtemp, 1, FUN = "MiseEnFormeKegg" ,FichierFinalNonQuote))
}else if (espece == "sce"){
suppressWarnings (apply (DTtemp, 1, FUN = "MiseEnFormeKeggSC" ,FichierFinalNonQuote))
}
if ( espece == "hsa" ) {
HS.KEGG.file.annot <<- read.table ( file = FichierFinalNonQuote ,na.strings = "",fill=TRUE,colClasses="character",sep= "\t",header = FALSE,quote = "",comment.char = "")
write.table (HS.KEGG.file.annot , FichierFinal ,col.names =FALSE,row.names=FALSE,append = TRUE, sep= "\t")
} else if ( espece == "mmu"){
MM.KEGG.file.annot <<- read.table ( file = FichierFinalNonQuote ,na.strings = "",fill=TRUE,colClasses="character",sep= "\t",header = FALSE,quote = "",comment.char = "")
write.table (MM.KEGG.file.annot , FichierFinal ,col.names =FALSE,row.names=FALSE,append = TRUE, sep= "\t")
}else if(espece == "sce"){
SC.KEGG.file.annot <<- read.table ( file = FichierFinalNonQuote ,na.strings = "",fill=TRUE,colClasses="character",sep= "\t",header = FALSE,quote = "",comment.char = "")
DTLL <- GeneInfoSC()
DTLL <- as.matrix(DTLL[DTLL[,1] == "4932",])
rownames(DTLL) <- as.character(DTLL[,4])
SC.KEGG.file.annot <<- as.matrix(SC.KEGG.file.annot)
rownames(SC.KEGG.file.annot) <<- as.character(SC.KEGG.file.annot[,1])
x <- DTLL[DTLL[,4] %in% as.character(SC.KEGG.file.annot[,1]),2]
SC.KEGG.file.annot <<- SC.KEGG.file.annot[SC.KEGG.file.annot[,1] %in% names(x),]
y <- NULL
for(i in 1:nrow(SC.KEGG.file.annot)){
y <- rbind(y,c(x[SC.KEGG.file.annot[i,1]],SC.KEGG.file.annot[i,2]))
}
colnames(y) <- as.character(matrix("",1,ncol(y)))
SC.KEGG.file.annot <<- y
write.table (SC.KEGG.file.annot , FichierFinal ,col.names =FALSE, row.names=FALSE,append = TRUE, sep= "\t")
}
close (FichierFinalNonQuote)
unlink(paste(getwd(),"/Annotations/KEGG/",DIResp,"/ll_keggNonQuote.txt",sep=""))
close (FichierFinal)
}
Kegg <- function () {
dir.create(paste(getwd(),"/Annotations/KEGG",sep=""))
download.file ( "ftp://ftp.genome.ad.jp/pub/kegg/pathway/map_title.tab" ,paste(getwd(), "/Annotations/KEGG/Temp_kegg_terms.txt",sep=""), mode = "w" )
temp <- file (paste(getwd(),"/Annotations/KEGG/Temp_kegg_terms.txt",sep=""),"r")
Fichkeggterms <- file (paste(getwd(),"/Annotations/KEGG/kegg_terms.txt",sep=""),"w")
KEGG.terms.name <<- read.table (file = temp ,na.strings = "",fill=TRUE,colClasses="character",sep= "\t",header = FALSE,quote = "",comment.char = "")
write.table ( KEGG.terms.name, Fichkeggterms ,col.names =FALSE,row.names=FALSE, sep = "\t")
close (temp)
close (Fichkeggterms)
unlink ( paste(getwd(),"/Annotations/KEGG/Temp_kegg_terms.txt",sep=""))
dir.create (paste(getwd(),"/Annotations/KEGG/HS",sep=""))
ChargerKegg ("hsa")
dir.create (paste(getwd(),"/Annotations/KEGG/MM",sep=""))
ChargerKegg ("mmu")
dir.create (paste(getwd(),"/Annotations/KEGG/SC",sep=""))
ChargerKegg ("sce")
}
MakeGoTerms <- function (DTGoTermsAndIds) {
DTGoTermsAndIds <- DTGoTermsAndIds [ substr ( DTGoTermsAndIds[,1],1,1) != "!" ,]
dimens <- nrow(DTGoTermsAndIds)
DTGoTermsAndIds <- cbind.data.frame( DTGoTermsAndIds, row.names = c(1: dimens))
GO.terms.name <<- DTGoTermsAndIds [,1:2]
FichierFinal <- file (paste(getwd(),"/Annotations/GO/go_terms.txt",sep=""), "w")
write.table ( GO.terms.name , FichierFinal ,col.names =FALSE,row.names=FALSE, sep = "\t")
close ( FichierFinal )
}
MakeGoHierarchy <- function (DATE="") {
if(DATE == ""){
DATE <- Sys.time()
DATE <- substr( as.character(DATE),1,7)
DATE <- gsub("-","",DATE)
}
NomFichier <- paste ( "go_", DATE , "-termdb-tables.tar.gz" ,sep = "")
download.file(paste ("http://godatabase-archive.stanford.edu/latest/", NomFichier,sep = ""),paste (getwd(),"/go_DATE-termdb-tables.tar.gz",sep=""),mode="wb")
system("gunzip go_DATE-termdb-tables.tar.gz")
system("tar -xf go_DATE-termdb-tables.tar")
FichTerm2term <- file (paste(getwd(),"/go_",DATE,"-termdb-tables/term2term.txt",sep=""), "r")
FichTerm <- file (paste(getwd(),"/go_",DATE,"-termdb-tables/term.txt",sep=""), "r")
FichFinal <- file (paste(getwd(),"/Annotations/GO/go_hierarchy.txt",sep=""), "w")
DTterm2term <- read.table ( file = FichTerm2term ,na.strings = "",fill=TRUE,colClasses="character",col.names =c(1:5),sep= "\t",header = FALSE, quote = "",comment.char = "")
DTterm <- read.table ( file = FichTerm ,na.strings = "",fill=TRUE,colClasses="character",col.names =c(1:6),sep= "\t",header = FALSE, quote = "",comment.char = "")
GO.terms.hierarchy <<- cbind ( DTterm [ DTterm2term[,4],4],DTterm [ DTterm2term[,3],4] )
write.table ( GO.terms.hierarchy, FichFinal ,col.names =FALSE,row.names=FALSE, sep= "\t")
close ( FichTerm2term )
close(FichTerm )
close (FichFinal)
unlink (paste (getwd(),"/go_DATE-termdb-tables.tar",sep=""))
unlink (paste(getwd(),"/go_",DATE,"-termdb-tables",sep=""), recursive = TRUE)
return (GO.terms.hierarchy)
}
AnnotationIndirecte <- function (DTGOOntology,DTGOHierarchy , DIResp, NomFichFinal ) {
FichFinal <- file (paste(getwd(),"/Annotations/GO/",DIResp,"/IND/",NomFichFinal,".txt",sep= ""), "w")
DTIND <- merge ( DTGOOntology, DTGOHierarchy , by.x= 2,by.y = 1)
names(DTIND)<-c("X0",names(DTGOOntology))
DTIND <- rbind.data.frame ( DTGOOntology, DTIND[,2:3] )
OrdreLignes <- do.call("order", DTIND[,c( 1,2)])
DTIND <- DTIND [ OrdreLignes,]
DTIND <- unique.data.frame (DTIND)
dimens <- nrow(DTIND)
DTIND <- cbind.data.frame( DTIND, row.names = c(1: dimens))
write.table ( DTIND, FichFinal ,col.names =FALSE,row.names=FALSE,sep="\t")
close( FichFinal )
return (DTIND)
}
TroisiemeFiltrage <- function (DTGoTermsAndIds,DTLoc2GoFiltre1, FichOntology ,initialeOntology) {
OntDTGoTermsAndIds <- DTGoTermsAndIds[ DTGoTermsAndIds[,3] == initialeOntology,]
DTOntology <- DTLoc2GoFiltre1 [ DTLoc2GoFiltre1[,2] %in% OntDTGoTermsAndIds[,1],]
DTOntology <- unique.data.frame (DTOntology)
OrdreLignes <- do.call("order", DTOntology[,c( 1,2)])
DTOntology <- DTOntology [ OrdreLignes,]
dimens <- nrow(DTOntology)
DTOntology <- cbind.data.frame( DTOntology, row.names = c(1: dimens))
write.table ( DTOntology, FichOntology ,col.names =FALSE,row.names=FALSE,sep="\t")
return (DTOntology)
}
GeneInfo <- function(){
download.file ( paste("ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz",sep="") ,paste( getwd(),"/Annotations/Temp.gz",sep=""), mode = "wb" )
LLTempgz <- gzfile (paste(getwd(),"/Annotations/Temp.gz",sep=""),"rb")
LLTemp <- file (paste(getwd(),"/Annotations/Temp.txt",sep=""), "w+")
vecTemp <- readLines(LLTempgz)
cat ( vecTemp , file = LLTemp, sep = "\n")
rm(vecTemp)
DTLLbrut <- read.table ( file = LLTemp,na.strings = "-",fill=TRUE,colClasses="character",sep= "\t",header = FALSE, quote = "",comment.char = "#")
DTLL <- cbind(DTLLbrut[,1],DTLLbrut[,2],DTLLbrut[,7],DTLLbrut[,8],DTLLbrut[,9])
close(LLTempgz)
close (LLTemp)
unlink (paste(getwd(),"/Annotations/Temp.gz",sep=""))
unlink (paste(getwd(),"/Annotations/Temp.txt",sep=""))
return (DTLL)
}
GeneInfoSC <- function(){
download.file ( paste("ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz",sep="") ,paste( getwd(),"/Annotations/Temp.gz",sep=""), mode = "wb" )
LLTempgz <- gzfile (paste(getwd(),"/Annotations/Temp.gz",sep=""),"rb")
LLTemp <- file (paste(getwd(),"/Annotations/Temp.txt",sep=""), "w+")
vecTemp <- readLines(LLTempgz)
cat ( vecTemp , file = LLTemp, sep = "\n")
rm(vecTemp)
DTLLbrut <- read.table ( file = LLTemp,na.strings = "-",fill=TRUE ,colClasses="character",sep= "\t",header = FALSE, quote = "",comment.char = "#")
DTLL <- cbind(DTLLbrut[,1],DTLLbrut[,2],DTLLbrut[,3],DTLLbrut[,4],DTLLbrut[,7],DTLLbrut[,8],DTLLbrut[,9])
close(LLTempgz)
close (LLTemp)
unlink (paste(getwd(),"/Annotations/Temp.gz",sep=""))
unlink (paste(getwd(),"/Annotations/Temp.txt",sep=""))
return (DTLL)
}
MakeCorrespondanceLLGO <- function (DTLoc2Go, DTGoTermsAndIds,DTGOHierarchy, espece = espece) {
if ( espece == "hs" ) {
DIResp <- "HS"
DTLoc2Go <- DTLoc2Go[DTLoc2Go[,1] == "9606",2:3]
} else {
if ( espece == "mm"){
DIResp <- "MM"
DTLoc2Go <- DTLoc2Go[DTLoc2Go[,1] == "10090",2:3]
}else if (espece == "sc"){
DIResp <- "SC"
DTLoc2Go <- DTLoc2Go[DTLoc2Go[,1] == "4932",2:3]
}
}
FichBioProcess <- file (paste(getwd(),"/Annotations/GO/",DIResp,"/DIR/biological_process.txt",sep= ""), "w")
FichCellComp <- file (paste(getwd(),"/Annotations/GO/",DIResp,"/DIR/cellular_component.txt",sep= ""), "w")
FichMolFunc <- file (paste(getwd(),"/Annotations/GO/",DIResp,"/DIR/molecular_function.txt",sep= ""), "w")
DTLoc2GoFiltre1 <- DTLoc2Go[ DTLoc2Go[,2] %in% DTGoTermsAndIds[,1],1:2]
if ( espece == "hs" ) {
HS.GO.DIR.BP.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichBioProcess ,"P")
HS.GO.DIR.CC.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichCellComp ,"C")
HS.GO.DIR.MF.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichMolFunc ,"F")
HS.GO.IND.BP.file.annot <<- AnnotationIndirecte (HS.GO.DIR.BP.file.annot,DTGOHierarchy,DIResp,"biological_process")
HS.GO.IND.CC.file.annot <<- AnnotationIndirecte (HS.GO.DIR.CC.file.annot,DTGOHierarchy,DIResp,"cellular_component")
HS.GO.IND.MF.file.annot <<- AnnotationIndirecte (HS.GO.DIR.MF.file.annot,DTGOHierarchy,DIResp,"molecular_function")
} else {
if ( espece == "mm"){
MM.GO.DIR.BP.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichBioProcess ,"P")
MM.GO.DIR.CC.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichCellComp ,"C")
MM.GO.DIR.MF.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichMolFunc ,"F")
MM.GO.IND.BP.file.annot <<- AnnotationIndirecte (MM.GO.DIR.BP.file.annot,DTGOHierarchy,DIResp,"biological_process")
MM.GO.IND.CC.file.annot <<- AnnotationIndirecte (MM.GO.DIR.CC.file.annot,DTGOHierarchy,DIResp,"cellular_component")
MM.GO.IND.MF.file.annot <<- AnnotationIndirecte (MM.GO.DIR.MF.file.annot,DTGOHierarchy,DIResp,"molecular_function")
}else if(espece == "sc"){
SC.GO.DIR.BP.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichBioProcess ,"P")
SC.GO.DIR.CC.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichCellComp ,"C")
SC.GO.DIR.MF.file.annot <<- TroisiemeFiltrage (DTGoTermsAndIds,DTLoc2GoFiltre1, FichMolFunc ,"F")
SC.GO.IND.BP.file.annot <<- AnnotationIndirecte (SC.GO.DIR.BP.file.annot,DTGOHierarchy,DIResp,"biological_process")
SC.GO.IND.CC.file.annot <<- AnnotationIndirecte (SC.GO.DIR.CC.file.annot,DTGOHierarchy,DIResp,"cellular_component")
SC.GO.IND.MF.file.annot <<- AnnotationIndirecte (SC.GO.DIR.MF.file.annot,DTGOHierarchy,DIResp,"molecular_function")
}
}
close(FichBioProcess)
close(FichCellComp)
close (FichMolFunc)
}
MakeLocusNames <- function( espece, DTLL ) {
if ( espece == "hs" ) {
DTLLesp <- DTLL[DTLL[,1] == "9606",2:5]
DIResp <- "HS"
} else {
if ( espece == "mm"){
DTLLesp <- DTLL[DTLL[,1] == "10090",2:5]
DIResp <- "MM"
}else if(espece == "sc"){
DTLLesp <- DTLL[DTLL[,1] == "4932",2:5]
DIResp <- "SC"
}
}
DTLLloc <- DTLLesp[, c(1,2,3)]
DTLLloc <- unique.data.frame (DTLLloc)
dimens <- nrow(DTLLloc)
DTLLloc <- cbind.data.frame( DTLLloc, row.names = c(1: dimens)) #
DTLLloc <- DTLLloc[2:nrow(DTLLloc),]
FichierLocation <- file (paste(getwd(),"/Annotations/LL/",DIResp,"/location.txt",sep= ""), "w")
write.table ( DTLLloc, FichierLocation ,col.names =FALSE,row.names=FALSE, sep="\t")
DTLLesp <- DTLLesp[, c(1,4)]
DTLLesp <- unique.data.frame (DTLLesp)
dimens <- nrow(DTLLesp)
DTLLesp <- cbind.data.frame( DTLLesp, row.names = c(1: dimens))
DTLLesp <- DTLLesp[2:nrow(DTLLesp),]
FichierFinal <- file (paste(getwd(),"/Annotations/LL/",DIResp,"/locus_name.txt",sep= ""), "w")
write.table ( DTLLesp, FichierFinal ,col.names =FALSE,row.names=FALSE, sep="\t")
if ( espece == "hs" ) {
HS.locus.name <<- DTLLesp
HS.locus.cyto <<- DTLLloc
} else {
if ( espece == "mm"){
MM.locus.name <<- DTLLesp
MM.locus.cyto <<- DTLLloc
}else if(espece == "sc"){
SC.locus.name <<- DTLLesp
SC.locus.cyto <<- DTLLloc
}
}
close ( FichierFinal )
close(FichierLocation)
}
goAndLL <- function (DATE="") {
dir.create (paste(getwd(),"/Annotations/GO",sep=""))
download.file ( "http://www.geneontology.org/doc/GO.terms_and_ids" ,paste(getwd(),"/Annotations/GO/GoTermsTmp.txt",sep=""), mode = "w" )
FichGoTermsAndIds <- file (paste(getwd(),"/Annotations/GO/GoTermsTmp.txt",sep=""), "r")
DTGoTermsAndIds <- read.table ( file = FichGoTermsAndIds ,na.strings = "",fill=TRUE,colClasses="character",col.names =c(1:3),sep= "\t",header = FALSE, quote = "",comment.char = "")
close(FichGoTermsAndIds)
unlink(paste(getwd(),"/Annotations/GO/GoTermsTmp.txt",sep=""))
download.file ( "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz" ,paste(getwd(),"/Annotations/GO/gene2go.gz",sep=""), mode = "wb" )
Gene2GOTempgz <- gzfile (paste(getwd(),"/Annotations/GO/gene2go.gz",sep=""),"rb")
Gene2GOTemp <- file (paste(getwd(),"/Annotations/GO/gene2go.txt",sep=""), "w+")
vecTemp <- readLines(Gene2GOTempgz)
cat ( vecTemp , file = Gene2GOTemp, sep = "\n")
DTLoc2Go <- read.table ( file = Gene2GOTemp,na.strings = "",fill=TRUE ,colClasses="character",col.names =c(1:8),sep= "\t",header = FALSE, quote = "",comment.char = "#")
close (Gene2GOTemp)
unlink(paste(getwd(),"/Annotations/GO/gene2go.txt",sep=""))
close (Gene2GOTempgz)
unlink(paste(getwd(),"/Annotations/GO/gene2go.gz",sep=""))
MakeGoTerms (DTGoTermsAndIds)
DTGoHierarchy <- MakeGoHierarchy (DATE=DATE)
DTLL <- GeneInfo()
dir.create (paste(getwd(),"/Annotations/GO/HS",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/HS/DIR",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/HS/IND",sep=""))
MakeCorrespondanceLLGO (DTLoc2Go,DTGoTermsAndIds, DTGoHierarchy , "hs")
dir.create (paste(getwd(),"/Annotations/GO/MM",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/MM/DIR",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/MM/IND",sep=""))
MakeCorrespondanceLLGO (DTLoc2Go, DTGoTermsAndIds, DTGoHierarchy , "mm")
dir.create (paste(getwd(),"/Annotations/GO/SC",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/SC/DIR",sep=""))
dir.create (paste(getwd(),"/Annotations/GO/SC/IND",sep=""))
MakeCorrespondanceLLGO (DTLoc2Go, DTGoTermsAndIds, DTGoHierarchy , "sc")
dir.create(paste(getwd(),"/Annotations/LL",sep=""))
dir.create (paste(getwd(),"/Annotations/LL/HS",sep=""))
MakeLocusNames ( "hs", DTLL)
dir.create (paste(getwd(),"/Annotations/LL/MM",sep=""))
MakeLocusNames ( "mm", DTLL)
dir.create (paste(getwd(),"/Annotations/LL/SC",sep=""))
MakeLocusNames ( "sc", DTLL)
}
annotations <- function (date.annot="") {
dir.create (paste (getwd(),"/Annotations", sep= ""))
Kegg ()
goAndLL(DATE=date.annot)
annot.date <- format(Sys.time(), "%Y %b %d")
# GO.terms.hierarchy <-GO.terms.hierarchy[(GO.terms.hierarchy[,1] %in% GO.terms.name[,1]) && (GO.terms.hierarchy[,2] %in% GO.terms.name[,1]),]
#
# HS.GO.DIR.BP.file.annot <- HS.GO.DIR.BP.file.annot[(HS.GO.DIR.BP.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.DIR.BP.file.annot[,1] %in% HS.locus.name[,1]),]
# HS.GO.DIR.CC.file.annot <- HS.GO.DIR.CC.file.annot[(HS.GO.DIR.CC.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.DIR.CC.file.annot[,1] %in% HS.locus.name[,1]),]
# HS.GO.DIR.MF.file.annot <- HS.GO.DIR.MF.file.annot[(HS.GO.DIR.MF.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.DIR.MF.file.annot[,1] %in% HS.locus.name[,1]),]
# HS.GO.IND.BP.file.annot <- HS.GO.IND.BP.file.annot[(HS.GO.IND.BP.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.IND.BP.file.annot[,1] %in% HS.locus.name[,1]),]
# HS.GO.IND.CC.file.annot <- HS.GO.IND.CC.file.annot[(HS.GO.IND.CC.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.IND.CC.file.annot[,1] %in% HS.locus.name[,1]),]
# HS.GO.IND.MF.file.annot <- HS.GO.IND.MF.file.annot[(HS.GO.IND.MF.file.annot[,2] %in% GO.terms.name[,1]) & (HS.GO.IND.MF.file.annot[,1] %in% HS.locus.name[,1]),]
#
# MM.GO.DIR.BP.file.annot <- MM.GO.DIR.BP.file.annot[(MM.GO.DIR.BP.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.DIR.BP.file.annot[,1] %in% MM.locus.name[,1]),]
# MM.GO.DIR.CC.file.annot <- MM.GO.DIR.CC.file.annot[(MM.GO.DIR.CC.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.DIR.CC.file.annot[,1] %in% MM.locus.name[,1]),]
# MM.GO.DIR.MF.file.annot <- MM.GO.DIR.MF.file.annot[(MM.GO.DIR.MF.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.DIR.MF.file.annot[,1] %in% MM.locus.name[,1]),]
# MM.GO.IND.BP.file.annot <- MM.GO.IND.BP.file.annot[(MM.GO.IND.BP.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.IND.BP.file.annot[,1] %in% MM.locus.name[,1]),]
# MM.GO.IND.CC.file.annot <- MM.GO.IND.CC.file.annot[(MM.GO.IND.CC.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.IND.CC.file.annot[,1] %in% MM.locus.name[,1]),]
# MM.GO.IND.MF.file.annot <- MM.GO.IND.MF.file.annot[(MM.GO.IND.MF.file.annot[,2] %in% GO.terms.name[,1]) & (MM.GO.IND.MF.file.annot[,1] %in% MM.locus.name[,1]),]
#
# SC.GO.DIR.BP.file.annot <- SC.GO.DIR.BP.file.annot[(SC.GO.DIR.BP.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.DIR.BP.file.annot[,1] %in% SC.locus.name[,1]),]
# SC.GO.DIR.CC.file.annot <- SC.GO.DIR.CC.file.annot[(SC.GO.DIR.CC.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.DIR.CC.file.annot[,1] %in% SC.locus.name[,1]),]
# SC.GO.DIR.MF.file.annot <- SC.GO.DIR.MF.file.annot[(SC.GO.DIR.MF.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.DIR.MF.file.annot[,1] %in% SC.locus.name[,1]),]
# SC.GO.IND.BP.file.annot <- SC.GO.IND.BP.file.annot[(SC.GO.IND.BP.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.IND.BP.file.annot[,1] %in% SC.locus.name[,1]),]
# SC.GO.IND.CC.file.annot <- SC.GO.IND.CC.file.annot[(SC.GO.IND.CC.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.IND.CC.file.annot[,1] %in% SC.locus.name[,1]),]
# SC.GO.IND.MF.file.annot <- SC.GO.IND.MF.file.annot[(SC.GO.IND.MF.file.annot[,2] %in% GO.terms.name[,1]) & (SC.GO.IND.MF.file.annot[,1] %in% SC.locus.name[,1]),]
save(GO.terms.hierarchy,GO.terms.name,HS.GO.DIR.BP.file.annot,HS.GO.DIR.CC.file.annot,HS.GO.DIR.MF.file.annot,
HS.GO.IND.BP.file.annot,HS.GO.IND.CC.file.annot,HS.GO.IND.MF.file.annot,HS.KEGG.file.annot,HS.locus.name,HS.locus.cyto,KEGG.terms.name,
MM.GO.DIR.BP.file.annot,MM.GO.DIR.CC.file.annot,MM.GO.DIR.MF.file.annot,MM.GO.IND.BP.file.annot,MM.GO.IND.CC.file.annot,
MM.GO.IND.MF.file.annot,MM.KEGG.file.annot,MM.locus.name,MM.locus.cyto,SC.GO.DIR.BP.file.annot,SC.GO.DIR.CC.file.annot,SC.GO.DIR.MF.file.annot,
SC.GO.IND.BP.file.annot,SC.GO.IND.CC.file.annot,SC.GO.IND.MF.file.annot,SC.KEGG.file.annot,SC.locus.name,SC.locus.cyto,
annot.date,file="sysdata.rda",compress=TRUE)
q(save="no")
}
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