Nothing
R/getListProfData.R
In canceR: A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
Defines functions
getListProfData
Documented in
getListProfData
#' get a list of Profile Data of every available dimensions. This function load matrices of every dimension (Exp, CNA, Met, RPPA,miRNA,Mut) and save them in a list for every disease.
#' @usage getListProfData()
#' @return a list of data frame with Profiles Data
#' @export
#' @examples
#' readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep=""))
#' \dontrun{
#' getListProfData()
#' head(myGlobalEnv$ProfData$Expression)
#' }
getListProfData <- function(){
## Testing The existing Cases and GenProf cgdsr references and getProfileData
grepRef<-function(regex1, listRef1,regex2, listRef2, GeneList,Mut){
if(length(grep(regex1,listRef1)) != 0){
if(length(grep(regex2,listRef2))!= 0){
if(Mut== 0){
print(paste("Getting Profile Data of ",regex2,"...",sep=""))
ProfData_X <- getProfileData(myGlobalEnv$cgds,GeneList, regex2,regex1)
########################
#ProfData_X <- ProfData_X[,as.factor(myGlobalEnv$GeneList)]
#ProfData_X <- ProfData_X[myGlobalEnv$GeneList,,drop=FALSE]
# > myGlobalEnv$GeneList[c(179,306,338,400)]
# [1] "HBXIP" "C16orf5" "SELS" "MAGI2-IT1"
# > colnames(ProfData)[c(82,198,205,404)]
# [1] "CDIP1" "LAMTOR5" "MAGI2.IT1" "VIMP"
# >
####################
if(length(ProfData_X)== 0){
if(length(myGlobalEnv$GeneList) <= 500){
## built empty data frame with gene Symbol in colnames
ProfData_X <- as.data.frame(setNames(replicate(length(myGlobalEnv$GeneList),numeric(1), simplify = FALSE), myGlobalEnv$GeneList[order(myGlobalEnv$GeneList)]))
return(ProfData_X)
}else{
ProfData_X <- as.data.frame(setNames(replicate(length(SubMegaGeneList),numeric(1), simplify = FALSE), SubMegaGeneList[order(SubMegaGeneList)]))
return(ProfData_X)
}
}else{
return(ProfData_X)
}
}else if(Mut==1){
print(paste("Getting Mutation Data of ",myGlobalEnv$checked_Studies[i],"...",sep=""))
MutData <- getMutationData(myGlobalEnv$cgds,regex1, regex2, GeneList)
print(paste("MutData: ",dim(MutData)))
if(length(MutData)==0){
## built emty data.frame as the same form of MutData
MutData <- data.frame("gene_symbol"=character(1),"mutation_type"=character(1), "amino_acid_change"=character(1))
return(MutData)
}else{
## From Mut Data frame select only Gene_symbol, Mutation_Type, AA-Changes
#myGlobalEnv$ListMutData[[StudiesRef[Si]]] <- MutData[,c(2,6,8)]# Gene Symbol, Mut type, AA change
return(MutData)
}
#return(MutData)
}
}else{tkmessageBox(message = paste("There is no genetic Profiles: ", regex2," for Study:",myGlobalEnv$checked_Studies[i] ), icon="warning" )
print(paste("There is no genetic Profile: ", regex2," for Study:",myGlobalEnv$checked_Studies[i],"..." ))
## built empty data frame with gene Symbol in colnames
if(length(myGlobalEnv$GeneList) <500){
ProfData_X <- as.data.frame(setNames(replicate(length(myGlobalEnv$GeneList),numeric(1), simplify = FALSE), myGlobalEnv$GeneList[order(myGlobalEnv$GeneList)]))
return(ProfData_X)
}else{
ProfData_X <- as.data.frame(setNames(replicate(length(SubMegaGeneList),numeric(1), simplify = FALSE), SubMegaGeneList[order(SubMegaGeneList)]))
return(ProfData_X)
}
return( ProfData_X)
}
}else{
tkmessageBox(message = paste("There is no Cases: ",regex1, " for Study:",myGlobalEnv$checked_Studies[i] ), icon="warning" )
print(paste("There is no Cases: ", regex1," for Study:",myGlobalEnv$checked_Studies[i],"..." ))
## built empty data frame with gene Symbol in colnames
if(length(myGlobalEnv$GeneList) <500){
ProfData_X <-as.data.frame(setNames(replicate(length(myGlobalEnv$GeneList),numeric(1), simplify = FALSE), myGlobalEnv$GeneList[order(myGlobalEnv$GeneList)]))
return(ProfData_X)
}else{
ProfData_X <-as.data.frame(setNames(replicate(length(SubMegaGeneList),numeric(1), simplify = FALSE), SubMegaGeneList[order(SubMegaGeneList)]))
return(ProfData_X)
}
return(ProfData_X)
}
}
if(exists("ListProfData", envir = myGlobalEnv)){
rm(ListProfData, envir=myGlobalEnv)
}
if(exists("ListMetData", envir = myGlobalEnv)){
rm(ListMetData, envir=myGlobalEnv)
}
if(exists("ListMutData", envir = myGlobalEnv)){
rm(ListMutData, envir=myGlobalEnv)
}
Lchecked_Studies <- myGlobalEnv$lchecked_Studies_forCases
#get Study references
StudiesRef <- getCancerStudies(myGlobalEnv$cgds)[,1]
LengthGenProfs <- 0
LengthCases <- 0
for (i in 1: Lchecked_Studies){
Si = myGlobalEnv$checked_StudyIndex[i]
progressBar_ProfilesData <- tkProgressBar(title = myGlobalEnv$Studies[Si], min = 0,
max = Lchecked_Studies, width = 400)
Sys.sleep(0.1)
setTkProgressBar(progressBar_ProfilesData, i, label=paste( round(i/Lchecked_Studies*100, 0),
"% of Profiles Data"))
### get Cases and Genetic Profiles with cgdsr references
GenProf_CNA<- paste(myGlobalEnv$checked_Studies[i],"_gistic", sep="")
Case_CNA <- paste(myGlobalEnv$checked_Studies[i],"_cna", sep="")
GenProf_Exp<- paste(myGlobalEnv$checked_Studies[i],"_rna_seq_v2_mrna", sep="")
Case_Exp <- paste(myGlobalEnv$checked_Studies[i],"_rna_seq_v2_mrna", sep="")
GenProf_Met_HM450<- paste(myGlobalEnv$checked_Studies[i],"_methylation_hm450", sep="")
Case_Met_HM450 <- paste(myGlobalEnv$checked_Studies[i],"_methylation_hm450", sep="")
GenProf_Met_HM27<- paste(myGlobalEnv$checked_Studies[i],"_methylation_hm27", sep="")
Case_Met_HM27 <- paste(myGlobalEnv$checked_Studies[i],"_methylation_hm27", sep="")
GenProf_RPPA<- paste(myGlobalEnv$checked_Studies[i],"_RPPA_protein_level", sep="")
Case_RPPA <- paste(myGlobalEnv$checked_Studies[i],"_rppa", sep="")
GenProf_miRNA<- paste(myGlobalEnv$checked_Studies[i],"_mirna", sep="")
Case_miRNA <- paste(myGlobalEnv$checked_Studies[i],"_microrna", sep="")
GenProf_Mut<- paste(myGlobalEnv$checked_Studies[i],"_mutations", sep="")
Case_Mut <- paste(myGlobalEnv$checked_Studies[i],"_sequenced", sep="")
## Subsettint of Gene List if bigger than 500
if(length(myGlobalEnv$GeneList)>500){
MegaGeneList <- myGlobalEnv$GeneList
if(is.integer(length(MegaGeneList)/500)){
G <- lenght(MegaGeneList)/500
}else{
G <- as.integer(length(MegaGeneList)/500) + 1
}
MegaProfData_CNA <- 0
MegaProfData_Exp <- 0
MegaProfData_Met_HM450 <- 0
MegaProfData_Met_HM27 <- 0
MegaProfData_RPPA <- 0
MegaProfData_miRNA <- 0
MegaMutData <- 0
SubMegaGeneList <- 0
LastSubMegaGeneList <- 0
for(g in 1: G){
if (length(MegaGeneList) - LastSubMegaGeneList > 500){
SubMegaGeneList <- MegaGeneList[((g-1)*(500)+1):((g)*500)]
LastSubMegaGeneList <- LastSubMegaGeneList + length(SubMegaGeneList)
print(paste("SubMega",g,length(SubMegaGeneList), sep=":"))
} else{
print(paste("SubMegaGeneList <-MegaGeneList[",LastSubMegaGeneList, ":", length(MegaGeneList),"]"))
SubMegaGeneList <- MegaGeneList[LastSubMegaGeneList:length(MegaGeneList)]
print(paste("SubMega else",g,length(SubMegaGeneList),sep=":"))
}
print("*************************************************")
print(paste("Getting Profile Data of Genes from: ", (((g-1)*500)+1), "to",((g-1)*500)+length(SubMegaGeneList),"of", myGlobalEnv$checked_Studies[i],sep= " "))
print("*************************************************")
ProfData_CNA<-grepRef(Case_CNA, myGlobalEnv$CasesRefStudies, GenProf_CNA, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
ProfData_Exp<-grepRef(Case_Exp, myGlobalEnv$CasesRefStudies, GenProf_Exp, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
ProfData_Met_HM450<-grepRef(Case_Met_HM450, myGlobalEnv$CasesRefStudies, GenProf_Met_HM450, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
print(paste("SubMega:",length(SubMegaGeneList)))
ProfData_Met_HM27<-grepRef(Case_Met_HM27, myGlobalEnv$CasesRefStudies, GenProf_Met_HM27, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
ProfData_RPPA<-grepRef(Case_RPPA, myGlobalEnv$CasesRefStudies, GenProf_RPPA, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
ProfData_miRNA<-grepRef(Case_miRNA, myGlobalEnv$CasesRefStudies, GenProf_miRNA, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
MutData <- grepRef(Case_Mut,myGlobalEnv$CasesRefStudies ,GenProf_Mut, myGlobalEnv$GenProfsRefStudies,SubMegaGeneList, Mut=1)
print("1")
MegaProfData_CNA <- cbind(MegaProfData_CNA, ProfData_CNA)
print("2")
MegaProfData_Exp <- cbind(MegaProfData_Exp, ProfData_Exp)
print("3")
MegaProfData_Met_HM450 <- cbind(MegaProfData_Met_HM450, ProfData_Met_HM450)
print("4")
MegaProfData_Met_HM27 <- cbind(MegaProfData_Met_HM27, ProfData_Met_HM27)
print("5")
MegaProfData_RPPA <- cbind(MegaProfData_RPPA, ProfData_RPPA)
print("6")
MegaProfData_miRNA <- cbind(MegaProfData_miRNA, ProfData_miRNA)
MegaMutData <- rbind(MegaMutData, MutData)
}
ProfData_CNA <- MegaProfData_CNA[,-1]
ProfData_Exp <- MegaProfData_Exp[,-1]
ProfData_Met_HM450 <- MegaProfData_Met_HM450[,-1]
ProfData_Met_HM27 <- MegaProfData_Met_HM27[,-1]
ProfData_RPPA <- MegaProfData_RPPA[,-1]
ProfData_miRNA <- MegaProfData_miRNA[,-1]
MutData <- MegaMutData[-1,]
} else if (length(myGlobalEnv$GeneList) > 0){
ProfData_CNA<- grepRef(Case_CNA, myGlobalEnv$CasesRefStudies, GenProf_CNA, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList, Mut=0)
ProfData_Exp<- grepRef(Case_Exp, myGlobalEnv$CasesRefStudies, GenProf_Exp, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList, Mut=0)
ProfData_Met_HM450 <- grepRef(Case_Met_HM450, myGlobalEnv$CasesRefStudies, GenProf_Met_HM450, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList, Mut=0)
ProfData_Met_HM27 <- grepRef(Case_Met_HM27, myGlobalEnv$CasesRefStudies, GenProf_Met_HM27, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList,Mut=0)
ProfData_RPPA<- grepRef(Case_RPPA, myGlobalEnv$CasesRefStudies, GenProf_RPPA, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList,Mut=0)
ProfData_miRNA<- grepRef(Case_miRNA, myGlobalEnv$CasesRefStudies, GenProf_miRNA, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList,Mut=0)
MutData <- grepRef(Case_Mut,myGlobalEnv$CasesRefStudies ,GenProf_Mut, myGlobalEnv$GenProfsRefStudies,myGlobalEnv$GeneList, Mut=1)
} else {
tkmessageBox(message= "Load gene List", icon="warning")
close(progressBar_ProfilesData)
stop("Load Gene List")
}
print("Saving... ")
myGlobalEnv$ListProfData$CNA[[StudiesRef[Si]]] <- ProfData_CNA
myGlobalEnv$ListProfData$Expression[[StudiesRef[Si]]] <- ProfData_Exp
myGlobalEnv$ListMetData$HM450[[StudiesRef[Si]]] <- ProfData_Met_HM450
myGlobalEnv$ListMetData$HM27[[StudiesRef[Si]]] <- ProfData_Met_HM27
myGlobalEnv$ListProfData$RPPA[[StudiesRef[Si]]] <- ProfData_RPPA
myGlobalEnv$ListProfData$miRNA[[StudiesRef[Si]]] <- ProfData_miRNA
myGlobalEnv$ListMutData[[StudiesRef[Si]]] <- MutData
print(" End Getting Profiles Data... ")
close(progressBar_ProfilesData)
}
# print("Start Ordering ...")
## range matrices by the same order
# myGlobalEnv$ListProfData$CNA <- myGlobalEnv$ListProfData$CNA[order(names(myGlobalEnv$ListProfData$CNA))]
# myGlobalEnv$ListProfData$Expression <- myGlobalEnv$ListProfData$Expression[order(names(myGlobalEnv$ListProfData$Expression))]
# myGlobalEnv$ListMetData$HM450 <- myGlobalEnv$ListMetData$HM450[order(names(myGlobalEnv$ListMetData$HM450))]
# myGlobalEnv$ListMetData$HM27 <- myGlobalEnv$ListMetData$HM27[order(names(myGlobalEnv$ListMetData$HM27))]
# myGlobalEnv$ListProfData$RPPA <- myGlobalEnv$ListProfData$RPPA[order(names(myGlobalEnv$ListProfData$RPPA))]
# myGlobalEnv$ListMutData <- myGlobalEnv$ListMutData[order(names(myGlobalEnv$ListMutData))]
# print("End Ordering ...")
## get Gene Mutation Frequency
UnifyRowNames <- function(x){
df_MutData <-as.data.frame(table(x$gene_symbol))
rownames(df_MutData) <- df_MutData$Var1
## ordering genes in MutData as in GeneList
df_GeneList <- as.data.frame(t(myGlobalEnv$GeneList))
#df_GeneList <- as.data.frame(myGlobalEnv$GeneList)
rownames(df_GeneList) <- df_GeneList[,1]
df_merge <- merge(df_GeneList, df_MutData, by="row.names",all.x=TRUE)
Freq_Mut <- df_merge[,c(-2,-3)]
return(Freq_Mut)
}
######
print("Start getting Frequency of Mutation ...")
#Freq_ListMutData <- plyr::laply(myGlobalEnv$ListMutData,function(x) UnifyRowNames(x))
Freq_ListMutData <- lapply(myGlobalEnv$ListMutData,
function(x) UnifyRowNames(x))
Freq_ArrayMutData <- array(unlist( Freq_ListMutData),
dim = c(nrow(Freq_ListMutData[[1]]),
ncol( Freq_ListMutData[[1]]),
length(Freq_ListMutData)))
if (inherits(try(dimnames(Freq_ArrayMutData) <-
list(Freq_ListMutData[[1]][,1],
colnames(Freq_ListMutData[[1]]),
names(Freq_ListMutData)),
silent=TRUE),"try-error")){
# p("There is a Study without Mutation Data.
# Use Mutation Panel to verify mutations data for selected studies.",
# align="center", style = "color:blue")
}else{
dimnames(Freq_ArrayMutData) <-
list(Freq_ListMutData[[1]][,1],
colnames(Freq_ListMutData[[1]]),
names(Freq_ListMutData))
}
# ?getListProfData(Genes= empty)
if(dim(Freq_ArrayMutData)[3]==1){
Freq_DfMutData <- as.numeric(Freq_ArrayMutData[,2,])
names(Freq_DfMutData) <- names(Freq_ArrayMutData[,2,])
## ordering gene list as in GeneList from MSigDB:
## grouping genes with the same biological process or gene Sets
Freq_DfMutData <- Freq_DfMutData[myGlobalEnv$GeneList]
Freq_DfMutData <- data.frame(round(Freq_DfMutData,digits=2))
names(Freq_DfMutData) <- names(Freq_ListMutData)
}else{
Freq_DfMutData <- apply(Freq_ArrayMutData[,2,],2,as.numeric)
rownames(Freq_DfMutData) <- rownames(Freq_ArrayMutData[,2,])
## ordering gene list as in GeneList from MSigDB:
## grouping genes with the same biological process or gene Sets
Freq_DfMutData <- Freq_DfMutData[myGlobalEnv$GeneList,,drop=FALSE]
Freq_DfMutData <- data.frame(round(Freq_DfMutData,digits=2))
}
myGlobalEnv$Freq_DfMutData <- Freq_DfMutData
print("End getting Mutation Frequency...")
######
#
# #output1 <- adply(Freq_ListMutData,1)
#
# ## convert the list of correlation matrices to Array
# Freq_ArrayMutData <- array(unlist( Freq_ListMutData), dim = c(nrow(Freq_ListMutData[[1]]), ncol( Freq_ListMutData[[1]]), length(Freq_ListMutData)))
# dimnames(Freq_ArrayMutData) <- list(Freq_ListMutData[[1]][,1], colnames(Freq_ListMutData[[1]]), names(Freq_ListMutData))
#
#
# Freq_DfMutData <- apply(Freq_ArrayMutData[,2,],2,as.numeric)
# rownames(Freq_DfMutData) <- rownames(Freq_ArrayMutData[,2,])
# ## ordering gene list as in GeneList from MSigDB: grouping genes with the same biological process or gene Sets
# Freq_DfMutData <- Freq_DfMutData[myGlobalEnv$GeneList,,drop=FALSE]
#
# myGlobalEnv$Freq_DfMutData <- Freq_DfMutData
#
# print("End getting Mutation Frequency...")
#
}
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Defines functions getListProfData
Documented in getListProfData
#' get a list of Profile Data of every available dimensions. This function load matrices of every dimension (Exp, CNA, Met, RPPA,miRNA,Mut) and save them in a list for every disease.
#' @usage getListProfData()
#' @return a list of data frame with Profiles Data
#' @export
#' @examples
#' readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep=""))
#' \dontrun{
#' getListProfData()
#' head(myGlobalEnv$ProfData$Expression)
#' }
getListProfData <- function(){
## Testing The existing Cases and GenProf cgdsr references and getProfileData
grepRef<-function(regex1, listRef1,regex2, listRef2, GeneList,Mut){
if(length(grep(regex1,listRef1)) != 0){
if(length(grep(regex2,listRef2))!= 0){
if(Mut== 0){
print(paste("Getting Profile Data of ",regex2,"...",sep=""))
ProfData_X <- getProfileData(myGlobalEnv$cgds,GeneList, regex2,regex1)
########################
#ProfData_X <- ProfData_X[,as.factor(myGlobalEnv$GeneList)]
#ProfData_X <- ProfData_X[myGlobalEnv$GeneList,,drop=FALSE]
# > myGlobalEnv$GeneList[c(179,306,338,400)]
# [1] "HBXIP" "C16orf5" "SELS" "MAGI2-IT1"
# > colnames(ProfData)[c(82,198,205,404)]
# [1] "CDIP1" "LAMTOR5" "MAGI2.IT1" "VIMP"
# >
####################
if(length(ProfData_X)== 0){
if(length(myGlobalEnv$GeneList) <= 500){
## built empty data frame with gene Symbol in colnames
ProfData_X <- as.data.frame(setNames(replicate(length(myGlobalEnv$GeneList),numeric(1), simplify = FALSE), myGlobalEnv$GeneList[order(myGlobalEnv$GeneList)]))
return(ProfData_X)
}else{
ProfData_X <- as.data.frame(setNames(replicate(length(SubMegaGeneList),numeric(1), simplify = FALSE), SubMegaGeneList[order(SubMegaGeneList)]))
return(ProfData_X)
}
}else{
return(ProfData_X)
}
}else if(Mut==1){
print(paste("Getting Mutation Data of ",myGlobalEnv$checked_Studies[i],"...",sep=""))
MutData <- getMutationData(myGlobalEnv$cgds,regex1, regex2, GeneList)
print(paste("MutData: ",dim(MutData)))
if(length(MutData)==0){
## built emty data.frame as the same form of MutData
MutData <- data.frame("gene_symbol"=character(1),"mutation_type"=character(1), "amino_acid_change"=character(1))
return(MutData)
}else{
## From Mut Data frame select only Gene_symbol, Mutation_Type, AA-Changes
#myGlobalEnv$ListMutData[[StudiesRef[Si]]] <- MutData[,c(2,6,8)]# Gene Symbol, Mut type, AA change
return(MutData)
}
#return(MutData)
}
}else{tkmessageBox(message = paste("There is no genetic Profiles: ", regex2," for Study:",myGlobalEnv$checked_Studies[i] ), icon="warning" )
print(paste("There is no genetic Profile: ", regex2," for Study:",myGlobalEnv$checked_Studies[i],"..." ))
## built empty data frame with gene Symbol in colnames
if(length(myGlobalEnv$GeneList) <500){
ProfData_X <- as.data.frame(setNames(replicate(length(myGlobalEnv$GeneList),numeric(1), simplify = FALSE), myGlobalEnv$GeneList[order(myGlobalEnv$GeneList)]))
return(ProfData_X)
}else{
ProfData_X <- as.data.frame(setNames(replicate(length(SubMegaGeneList),numeric(1), simplify = FALSE), SubMegaGeneList[order(SubMegaGeneList)]))
return(ProfData_X)
}
return( ProfData_X)
}
}else{
tkmessageBox(message = paste("There is no Cases: ",regex1, " for Study:",myGlobalEnv$checked_Studies[i] ), icon="warning" )
print(paste("There is no Cases: ", regex1," for Study:",myGlobalEnv$checked_Studies[i],"..." ))
## built empty data frame with gene Symbol in colnames
if(length(myGlobalEnv$GeneList) <500){
ProfData_X <-as.data.frame(setNames(replicate(length(myGlobalEnv$GeneList),numeric(1), simplify = FALSE), myGlobalEnv$GeneList[order(myGlobalEnv$GeneList)]))
return(ProfData_X)
}else{
ProfData_X <-as.data.frame(setNames(replicate(length(SubMegaGeneList),numeric(1), simplify = FALSE), SubMegaGeneList[order(SubMegaGeneList)]))
return(ProfData_X)
}
return(ProfData_X)
}
}
if(exists("ListProfData", envir = myGlobalEnv)){
rm(ListProfData, envir=myGlobalEnv)
}
if(exists("ListMetData", envir = myGlobalEnv)){
rm(ListMetData, envir=myGlobalEnv)
}
if(exists("ListMutData", envir = myGlobalEnv)){
rm(ListMutData, envir=myGlobalEnv)
}
Lchecked_Studies <- myGlobalEnv$lchecked_Studies_forCases
#get Study references
StudiesRef <- getCancerStudies(myGlobalEnv$cgds)[,1]
LengthGenProfs <- 0
LengthCases <- 0
for (i in 1: Lchecked_Studies){
Si = myGlobalEnv$checked_StudyIndex[i]
progressBar_ProfilesData <- tkProgressBar(title = myGlobalEnv$Studies[Si], min = 0,
max = Lchecked_Studies, width = 400)
Sys.sleep(0.1)
setTkProgressBar(progressBar_ProfilesData, i, label=paste( round(i/Lchecked_Studies*100, 0),
"% of Profiles Data"))
### get Cases and Genetic Profiles with cgdsr references
GenProf_CNA<- paste(myGlobalEnv$checked_Studies[i],"_gistic", sep="")
Case_CNA <- paste(myGlobalEnv$checked_Studies[i],"_cna", sep="")
GenProf_Exp<- paste(myGlobalEnv$checked_Studies[i],"_rna_seq_v2_mrna", sep="")
Case_Exp <- paste(myGlobalEnv$checked_Studies[i],"_rna_seq_v2_mrna", sep="")
GenProf_Met_HM450<- paste(myGlobalEnv$checked_Studies[i],"_methylation_hm450", sep="")
Case_Met_HM450 <- paste(myGlobalEnv$checked_Studies[i],"_methylation_hm450", sep="")
GenProf_Met_HM27<- paste(myGlobalEnv$checked_Studies[i],"_methylation_hm27", sep="")
Case_Met_HM27 <- paste(myGlobalEnv$checked_Studies[i],"_methylation_hm27", sep="")
GenProf_RPPA<- paste(myGlobalEnv$checked_Studies[i],"_RPPA_protein_level", sep="")
Case_RPPA <- paste(myGlobalEnv$checked_Studies[i],"_rppa", sep="")
GenProf_miRNA<- paste(myGlobalEnv$checked_Studies[i],"_mirna", sep="")
Case_miRNA <- paste(myGlobalEnv$checked_Studies[i],"_microrna", sep="")
GenProf_Mut<- paste(myGlobalEnv$checked_Studies[i],"_mutations", sep="")
Case_Mut <- paste(myGlobalEnv$checked_Studies[i],"_sequenced", sep="")
## Subsettint of Gene List if bigger than 500
if(length(myGlobalEnv$GeneList)>500){
MegaGeneList <- myGlobalEnv$GeneList
if(is.integer(length(MegaGeneList)/500)){
G <- lenght(MegaGeneList)/500
}else{
G <- as.integer(length(MegaGeneList)/500) + 1
}
MegaProfData_CNA <- 0
MegaProfData_Exp <- 0
MegaProfData_Met_HM450 <- 0
MegaProfData_Met_HM27 <- 0
MegaProfData_RPPA <- 0
MegaProfData_miRNA <- 0
MegaMutData <- 0
SubMegaGeneList <- 0
LastSubMegaGeneList <- 0
for(g in 1: G){
if (length(MegaGeneList) - LastSubMegaGeneList > 500){
SubMegaGeneList <- MegaGeneList[((g-1)*(500)+1):((g)*500)]
LastSubMegaGeneList <- LastSubMegaGeneList + length(SubMegaGeneList)
print(paste("SubMega",g,length(SubMegaGeneList), sep=":"))
} else{
print(paste("SubMegaGeneList <-MegaGeneList[",LastSubMegaGeneList, ":", length(MegaGeneList),"]"))
SubMegaGeneList <- MegaGeneList[LastSubMegaGeneList:length(MegaGeneList)]
print(paste("SubMega else",g,length(SubMegaGeneList),sep=":"))
}
print("*************************************************")
print(paste("Getting Profile Data of Genes from: ", (((g-1)*500)+1), "to",((g-1)*500)+length(SubMegaGeneList),"of", myGlobalEnv$checked_Studies[i],sep= " "))
print("*************************************************")
ProfData_CNA<-grepRef(Case_CNA, myGlobalEnv$CasesRefStudies, GenProf_CNA, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
ProfData_Exp<-grepRef(Case_Exp, myGlobalEnv$CasesRefStudies, GenProf_Exp, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
ProfData_Met_HM450<-grepRef(Case_Met_HM450, myGlobalEnv$CasesRefStudies, GenProf_Met_HM450, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
print(paste("SubMega:",length(SubMegaGeneList)))
ProfData_Met_HM27<-grepRef(Case_Met_HM27, myGlobalEnv$CasesRefStudies, GenProf_Met_HM27, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
ProfData_RPPA<-grepRef(Case_RPPA, myGlobalEnv$CasesRefStudies, GenProf_RPPA, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
ProfData_miRNA<-grepRef(Case_miRNA, myGlobalEnv$CasesRefStudies, GenProf_miRNA, myGlobalEnv$GenProfsRefStudies, SubMegaGeneList, Mut=0)
MutData <- grepRef(Case_Mut,myGlobalEnv$CasesRefStudies ,GenProf_Mut, myGlobalEnv$GenProfsRefStudies,SubMegaGeneList, Mut=1)
print("1")
MegaProfData_CNA <- cbind(MegaProfData_CNA, ProfData_CNA)
print("2")
MegaProfData_Exp <- cbind(MegaProfData_Exp, ProfData_Exp)
print("3")
MegaProfData_Met_HM450 <- cbind(MegaProfData_Met_HM450, ProfData_Met_HM450)
print("4")
MegaProfData_Met_HM27 <- cbind(MegaProfData_Met_HM27, ProfData_Met_HM27)
print("5")
MegaProfData_RPPA <- cbind(MegaProfData_RPPA, ProfData_RPPA)
print("6")
MegaProfData_miRNA <- cbind(MegaProfData_miRNA, ProfData_miRNA)
MegaMutData <- rbind(MegaMutData, MutData)
}
ProfData_CNA <- MegaProfData_CNA[,-1]
ProfData_Exp <- MegaProfData_Exp[,-1]
ProfData_Met_HM450 <- MegaProfData_Met_HM450[,-1]
ProfData_Met_HM27 <- MegaProfData_Met_HM27[,-1]
ProfData_RPPA <- MegaProfData_RPPA[,-1]
ProfData_miRNA <- MegaProfData_miRNA[,-1]
MutData <- MegaMutData[-1,]
} else if (length(myGlobalEnv$GeneList) > 0){
ProfData_CNA<- grepRef(Case_CNA, myGlobalEnv$CasesRefStudies, GenProf_CNA, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList, Mut=0)
ProfData_Exp<- grepRef(Case_Exp, myGlobalEnv$CasesRefStudies, GenProf_Exp, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList, Mut=0)
ProfData_Met_HM450 <- grepRef(Case_Met_HM450, myGlobalEnv$CasesRefStudies, GenProf_Met_HM450, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList, Mut=0)
ProfData_Met_HM27 <- grepRef(Case_Met_HM27, myGlobalEnv$CasesRefStudies, GenProf_Met_HM27, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList,Mut=0)
ProfData_RPPA<- grepRef(Case_RPPA, myGlobalEnv$CasesRefStudies, GenProf_RPPA, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList,Mut=0)
ProfData_miRNA<- grepRef(Case_miRNA, myGlobalEnv$CasesRefStudies, GenProf_miRNA, myGlobalEnv$GenProfsRefStudies, myGlobalEnv$GeneList,Mut=0)
MutData <- grepRef(Case_Mut,myGlobalEnv$CasesRefStudies ,GenProf_Mut, myGlobalEnv$GenProfsRefStudies,myGlobalEnv$GeneList, Mut=1)
} else {
tkmessageBox(message= "Load gene List", icon="warning")
close(progressBar_ProfilesData)
stop("Load Gene List")
}
print("Saving... ")
myGlobalEnv$ListProfData$CNA[[StudiesRef[Si]]] <- ProfData_CNA
myGlobalEnv$ListProfData$Expression[[StudiesRef[Si]]] <- ProfData_Exp
myGlobalEnv$ListMetData$HM450[[StudiesRef[Si]]] <- ProfData_Met_HM450
myGlobalEnv$ListMetData$HM27[[StudiesRef[Si]]] <- ProfData_Met_HM27
myGlobalEnv$ListProfData$RPPA[[StudiesRef[Si]]] <- ProfData_RPPA
myGlobalEnv$ListProfData$miRNA[[StudiesRef[Si]]] <- ProfData_miRNA
myGlobalEnv$ListMutData[[StudiesRef[Si]]] <- MutData
print(" End Getting Profiles Data... ")
close(progressBar_ProfilesData)
}
# print("Start Ordering ...")
## range matrices by the same order
# myGlobalEnv$ListProfData$CNA <- myGlobalEnv$ListProfData$CNA[order(names(myGlobalEnv$ListProfData$CNA))]
# myGlobalEnv$ListProfData$Expression <- myGlobalEnv$ListProfData$Expression[order(names(myGlobalEnv$ListProfData$Expression))]
# myGlobalEnv$ListMetData$HM450 <- myGlobalEnv$ListMetData$HM450[order(names(myGlobalEnv$ListMetData$HM450))]
# myGlobalEnv$ListMetData$HM27 <- myGlobalEnv$ListMetData$HM27[order(names(myGlobalEnv$ListMetData$HM27))]
# myGlobalEnv$ListProfData$RPPA <- myGlobalEnv$ListProfData$RPPA[order(names(myGlobalEnv$ListProfData$RPPA))]
# myGlobalEnv$ListMutData <- myGlobalEnv$ListMutData[order(names(myGlobalEnv$ListMutData))]
# print("End Ordering ...")
## get Gene Mutation Frequency
UnifyRowNames <- function(x){
df_MutData <-as.data.frame(table(x$gene_symbol))
rownames(df_MutData) <- df_MutData$Var1
## ordering genes in MutData as in GeneList
df_GeneList <- as.data.frame(t(myGlobalEnv$GeneList))
#df_GeneList <- as.data.frame(myGlobalEnv$GeneList)
rownames(df_GeneList) <- df_GeneList[,1]
df_merge <- merge(df_GeneList, df_MutData, by="row.names",all.x=TRUE)
Freq_Mut <- df_merge[,c(-2,-3)]
return(Freq_Mut)
}
######
print("Start getting Frequency of Mutation ...")
#Freq_ListMutData <- plyr::laply(myGlobalEnv$ListMutData,function(x) UnifyRowNames(x))
Freq_ListMutData <- lapply(myGlobalEnv$ListMutData,
function(x) UnifyRowNames(x))
Freq_ArrayMutData <- array(unlist( Freq_ListMutData),
dim = c(nrow(Freq_ListMutData[[1]]),
ncol( Freq_ListMutData[[1]]),
length(Freq_ListMutData)))
if (inherits(try(dimnames(Freq_ArrayMutData) <-
list(Freq_ListMutData[[1]][,1],
colnames(Freq_ListMutData[[1]]),
names(Freq_ListMutData)),
silent=TRUE),"try-error")){
# p("There is a Study without Mutation Data.
# Use Mutation Panel to verify mutations data for selected studies.",
# align="center", style = "color:blue")
}else{
dimnames(Freq_ArrayMutData) <-
list(Freq_ListMutData[[1]][,1],
colnames(Freq_ListMutData[[1]]),
names(Freq_ListMutData))
}
# ?getListProfData(Genes= empty)
if(dim(Freq_ArrayMutData)[3]==1){
Freq_DfMutData <- as.numeric(Freq_ArrayMutData[,2,])
names(Freq_DfMutData) <- names(Freq_ArrayMutData[,2,])
## ordering gene list as in GeneList from MSigDB:
## grouping genes with the same biological process or gene Sets
Freq_DfMutData <- Freq_DfMutData[myGlobalEnv$GeneList]
Freq_DfMutData <- data.frame(round(Freq_DfMutData,digits=2))
names(Freq_DfMutData) <- names(Freq_ListMutData)
}else{
Freq_DfMutData <- apply(Freq_ArrayMutData[,2,],2,as.numeric)
rownames(Freq_DfMutData) <- rownames(Freq_ArrayMutData[,2,])
## ordering gene list as in GeneList from MSigDB:
## grouping genes with the same biological process or gene Sets
Freq_DfMutData <- Freq_DfMutData[myGlobalEnv$GeneList,,drop=FALSE]
Freq_DfMutData <- data.frame(round(Freq_DfMutData,digits=2))
}
myGlobalEnv$Freq_DfMutData <- Freq_DfMutData
print("End getting Mutation Frequency...")
######
#
# #output1 <- adply(Freq_ListMutData,1)
#
# ## convert the list of correlation matrices to Array
# Freq_ArrayMutData <- array(unlist( Freq_ListMutData), dim = c(nrow(Freq_ListMutData[[1]]), ncol( Freq_ListMutData[[1]]), length(Freq_ListMutData)))
# dimnames(Freq_ArrayMutData) <- list(Freq_ListMutData[[1]][,1], colnames(Freq_ListMutData[[1]]), names(Freq_ListMutData))
#
#
# Freq_DfMutData <- apply(Freq_ArrayMutData[,2,],2,as.numeric)
# rownames(Freq_DfMutData) <- rownames(Freq_ArrayMutData[,2,])
# ## ordering gene list as in GeneList from MSigDB: grouping genes with the same biological process or gene Sets
# Freq_DfMutData <- Freq_DfMutData[myGlobalEnv$GeneList,,drop=FALSE]
#
# myGlobalEnv$Freq_DfMutData <- Freq_DfMutData
#
# print("End getting Mutation Frequency...")
#
}
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