Nothing
R/MetReportNames.R
In Metab: Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
MetReportNames <-
function (data, AmdisReport, base.peak = FALSE, save = TRUE, folder, output = "metab_data", TimeWindow = 2.5, Remove)
{
######################################################
############# Function to check if file is CDF #######
######################################################
isCDFdlg <- function(titleMSG, errorMSG) {
t = 0
while (t == 0) {
checkIfCDF <- dlgOpen(title = titleMSG, multiple = FALSE)$res
checkIfCDF2 <- basename(checkIfCDF)
checkIfCDF3 <- unlist(strsplit(checkIfCDF2, "\\."))
checkIfCDF4 <- checkIfCDF3[length(checkIfCDF3)]
if (checkIfCDF4 %in% c("CDF", "cdf")) {
t = 1
return(checkIfCDF)
} else {
dlgMessage(errorMSG)
}
}
}
#######################################################
################# Check if CDF - No dialog box ########
#######################################################
isCDF <- function(pathFile, errorMSG) {
t = 0
checkIfCDF <- pathFile
checkIfCDF2 <- basename(checkIfCDF)
checkIfCDF3 <- unlist(strsplit(checkIfCDF2, "\\."))
checkIfCDF4 <- checkIfCDF3[length(checkIfCDF3)]
if (checkIfCDF4 %in% c("CDF", "cdf")) {
t = 1
return(t)
} else {
#dlgMessage(errorMSG)
return(t)
}
}
######### Check if a CSV or .msl file ############
isCSVORmsldlg <- function(titleMSG, errorMSG){
t = 0
while (t == 0){
checkIfCsv <- dlgOpen(title = titleMSG, multiple = FALSE)$res
checkIfCsv2 <- basename(checkIfCsv)
checkIfCsv3 <- unlist(strsplit(checkIfCsv2, "\\."))
checkIfCsv4 <- checkIfCsv3[length(checkIfCsv3)]
if (checkIfCsv4 %in% c("CSV", "csv")){
t = 1
return(c(checkIfCsv, "csv"))
} else {
if (checkIfCsv4 %in% c("MSL", "msl")){
t = 1
return(c(checkIfCsv, "msl"))
} else {
dlgMessage(errorMSG)
}
}
}
}
####################################################
######### Check if a CSV or .msl file NO DIALOG BOX ############
isCSVORmsl <- function(pathfile, errorMSG){
t = 0
checkIfCsv2 <- basename(pathfile)
checkIfCsv3 <- unlist(strsplit(checkIfCsv2, "\\."))
checkIfCsv4 <- checkIfCsv3[length(checkIfCsv3)]
if (checkIfCsv4 %in% c("CSV", "csv")){
t = "csv"
return(t)
} else {
if (checkIfCsv4 %in% c("MSL", "msl")){
t = "msl"
return(t)
} else {
t = 0
return(t)
}
}
}
####################################################
##### If no AMDIS report specified ####
if (missing(AmdisReport)) {
AmdisReport <- dlgOpen(title = "Select the AMDIS report generated in batch mode")$res
AmdisReportUsed <- AmdisReport
AmdisReport = read.csv(AmdisReport, sep = "\t", colClass = "character")
} else {
if (is.data.frame(AmdisReport)) {
AmdisReportUsed <- "data_frame"
AmdisReport <- AmdisReport
message("AmdisReport - Data frame loaded...")
} else {
if (is.character(AmdisReport)) {
inputTest <- file.access(AmdisReport, 0)
if (inputTest == 0) {
AmdisReportUsed <- AmdisReport
AmdisReport = read.csv(AmdisReport, sep = "\t", colClasses = "character")
} else {
dlgMessage("The AmdisReport specified is not accessible. Please, select the AMDIS report generated in batch mode.")
AmdisReport <- dlgOpen(title = "Select the AMDIS report generated in batch mode")$res
AmdisReportUsed <- AmdisReport
AmdisReport = read.csv(AmdisReport, sep = "\t", colClass = "character")
}
} else {
dlgMessage("The AmdisReport specified is not valid. Please, select the AMDIS report generated in batch mode.")
AmdisReport <- dlgOpen(title = "Select the AMDIS report generated in batch mode")$res
AmdisReportUsed <- AmdisReport
AmdisReport = read.csv(AmdisReport, sep = "\t", colClass = "character")
}
}
}
total_report <- AmdisReport
if (missing(Remove)){
RemoveUsed <- "None"
} else {
RemoveUsed <- Remove
for (i in 1:length(Remove)){
toRemove <- grep(Remove[i], total_report$Name, ignore.case = FALSE, value = TRUE)
total_report <- subset(total_report, !(total_report$Name %in% toRemove))
}
}
######################################################
########## Collect Data ##############################
######################################################
if (missing(data)) {
filesToAnalyse <- total_report[1]
filesToAnalyse <- data.frame(filesToAnalyse[!duplicated(filesToAnalyse),], stringsAsFactors = FALSE)
filesToAnalyse <- data.frame(gsub("\\", "/", filesToAnalyse[,1], fixed = TRUE), stringsAsFactors = FALSE)
filesToAnalyse <- data.frame(apply(filesToAnalyse, 1, function(x) basename(as.character(x))), stringsAsFactors = FALSE)
filesToAnalyse[1] <- gsub(".FIN", "", filesToAnalyse[,1], fixed = TRUE)
data <- dlgList(filesToAnalyse[,1], multiple = TRUE, title = "Select the files to be analyzed.")$res
dataUsed <- data
} else {
if (is.character(data)) {
dataUsed <- data
dataUsed <- gsub(".FIN", "", dataUsed, fixed = TRUE)
} else {
message("data must be specified as character.")
filesToAnalyse <- total_report[1]
filesToAnalyse <- data.frame(filesToAnalyse[!duplicated(filesToAnalyse),], stringsAsFactors = FALSE)
filesToAnalyse <- data.frame(gsub("\\", "/", filesToAnalyse[,1], fixed = TRUE), stringsAsFactors = FALSE)
filesToAnalyse <- data.frame(apply(filesToAnalyse, 1, function(x) basename(as.character(x))), stringsAsFactors = FALSE)
filesToAnalyse[1] <- gsub(".FIN", "", filesToAnalyse[,1], fixed = TRUE)
data <- dlgList(filesToAnalyse[,1], multiple = TRUE, title = "Select the files to be analyzed.")$res
dataUsed <- data
}
}
######################################################
########## Collect Folder ############################
######################################################
if (save) {
if (missing(folder)) {
folder = dlgDir(title = "Select the folder where the output file will be saved.")$res
} else {
if (is.character(folder)) {
isFolder <- file.access(as.character(folder), 0)
if (isFolder == 0) {
isFolder <- file.info(folder)
if (!isFolder$isdir) {
folder = dlgDir(title = "Select the folder where the output file will be saved.")$res
}
} else {
folder = dlgDir(title = "Select the folder where the output file will be saved.")$res
}
} else {
folder = dlgDir(title = "Select the folder where the output file will be saved.")$res
}
}
}
#################################
###### Start analysis ###########
#################################
Result.df <- 1
for (i in 1:length(dataUsed)){
surefinal <- c()
file <- dataUsed[i]
name.file <- file
file <- paste(file, ".FIN", sep = "")
file <- grep(file, total_report$FileName, fixed = TRUE)
if (length(file) > 0) {
data.df <- total_report[file, ]
if (base.peak){
Keep <- c("Name", "RT", "Scan", "Expec..RT",
"Base.Peak")
AbundancesUsed <- "Base.Peak"
} else {
Keep <- c("Name", "RT", "Scan", "Expec..RT",
"Area")
AbundancesUsed <- "Area"
}
data.df <- data.df[, Keep]
data.df[2] <- as.numeric(data.df[,2])
data.df[3] <- as.numeric(data.df[,3])
data.df[4] <- as.numeric(data.df[,4])
data.df[5] <- as.numeric(data.df[,5])
data.df$deff <- data.df$RT - data.df$Expec..RT
data.df <- subset(data.df, data.df$deff < TimeWindow & data.df$deff > -TimeWindow)
while (nrow(data.df) != 0) {
line <- data.df[1, ]
sameRT <- subset(data.df, data.df$RT == line$RT)
data.df <- data.df[-which(row.names(data.df) %in% row.names(sameRT)),]
if (nrow(sameRT) > 1) {
doub <- grep("[?]", sameRT$Name, value = TRUE)
if (nrow(sameRT) == length(doub)) {
oneq <- grep("^?\\s", sameRT$Name, value = TRUE)
twoq <- grep("^??\\s", sameRT$Name, value = TRUE)
thrq <- grep("^???\\s", sameRT$Name, value = TRUE)
if (length(oneq) == 0) {
if (length(twoq) == 0) {
findCloser <- sameRT
findCloser$deff <- abs(findCloser$deff)
sure <- sameRT[which(findCloser$deff == min(findCloser$deff)),]
if (nrow(sure) > 1){
sure <- sameRT[which(sure$Base.Peak == max(sure$Base.Peak)),]
}
} else {
if (length(twoq) > 1) {
sameRT <- subset(sameRT, sameRT$Name %in% twoq)
findCloser <- sameRT
findCloser$deff <- abs(findCloser$deff)
sure <- sameRT[which(findCloser$deff == min(findCloser$deff)),]
if (nrow(sure) > 1){
sure <- sameRT[which(sure$Base.Peak == max(sure$Base.Peak)),]
}
} else {
sameRT <- subset(sameRT, sameRT$Name %in% twoq)
sure <- sameRT
}
}
} else {
if (length(oneq) > 1){
sameRT <- subset(sameRT, (sameRT$Name %in% oneq))
findCloser <- sameRT
findCloser$deff <- abs(findCloser$deff)
sure <- sameRT[which(findCloser$deff == min(findCloser$deff)),]
if (nrow(sure) > 1){
sure <- sameRT[which(sure$Base.Peak == max(sure$Base.Peak)),]
}
} else {
sameRT <- subset(sameRT, sameRT$Name %in% twoq)
sure <- sameRT
}
}
} else {
sameRT <- subset(sameRT, !(sameRT$Name %in% doub))
if (nrow(sameRT) > 1) {
findCloser <- sameRT
findCloser$deff <- abs(findCloser$deff)
sure <- sameRT[which(findCloser$deff == min(findCloser$deff)),]
if (nrow(sure) > 1){
preSure <- sameRT[which(sure$Base.Peak == max(sure$Base.Peak)),]
sure <- preSure[1,]
}
}
}
} else {
sure <- sameRT
}
if (length(surefinal) == 0){
surefinal <- sure
} else {
surefinal <- rbind(sure, surefinal)
}
}
surefinal <- surefinal[!duplicated(surefinal$RT),]
surefinal[1] <- gsub("? ", "", surefinal[,1], fixed = TRUE)
surefinal[1] <- gsub("?", "", surefinal[,1], fixed = TRUE)
names(surefinal)[5] <- name.file
dupli <- surefinal[duplicated(surefinal[,1]),]
if (nrow(dupli) > 0){
while(nrow(dupli) > 0){
checkDupli <- dupli[1,]
sameName <- subset(surefinal, surefinal$Name == checkDupli$Name)
sameName$deff <- abs(sameName$deff)
choseName <- sameName[which(sameName$deff == min(abs(sameName$deff), na.rm = TRUE)),]
if (nrow(choseName) > 1){
choseName <- choseName[which(choseName[,5] == max(choseName[,5], na.rm = TRUE)),]
}
sameName <- sameName[-(which(row.names(sameName) == row.names(choseName))),]
surefinal <- surefinal[-which(row.names(surefinal) %in% row.names(sameName)),]
dupli <- dupli[-(which(dupli$Name %in% checkDupli$Name)),]
}
}
if (Result.df == 1) {
final.df <- surefinal[c(1,5)]
confirmation <- paste("File", name.file, "done!", sep = " ")
message(confirmation)
Result.df <- Result.df + 1
} else {
surefinal <- surefinal[c(1,5)]
final.df <- merge(final.df, surefinal, by.x = "Name", by.y = "Name", all = TRUE)
confirmation <- paste("File", name.file, "done!", sep = " ")
message(confirmation)
}
} else {
confirmation <- paste("File ", name.file, " not analyzed! Probably there is no metabolites detected for this sample in the AMDIS report", sep = "")
message(confirmation)
final.df$error <- NA
names(final.df)[ncol(final.df)] <- name.file
}
}
final.df <- final.df[order(final.df[, 1], decreasing = F),]
if (save) {
sheet <- output
store <- file.path(folder, paste(sheet, ".csv", sep = ""))
inputTest <- file.access(store, 0)
if (inputTest == 0) {
addFile <- 1
while(inputTest == 0){
store <- file.path(folder, paste(sheet, addFile, ".csv", sep = ""))
inputTest <- file.access(store, 0)
addFile <- addFile + 1
}
}
write.csv(final.df, file = store, row.names = FALSE)
message("File saved: ", store, "\n")
##### Generate log file ######
logFile <- data.frame(Directory = data, Amdis_report = AmdisReportUsed, Output_file = store, Time_window = TimeWindow, Analysis_date = date(), Metabolites_removed = RemoveUsed, Abundances = AbundancesUsed)
sheet <- "logFile"
store <- file.path(folder, paste(sheet, ".csv", sep = ""))
inputTest <- file.access(store, 0)
if (inputTest == 0) {
addFile <- 1
while(inputTest == 0){
store <- file.path(folder, paste(sheet, addFile, ".csv", sep = ""))
inputTest <- file.access(store, 0)
addFile <- addFile + 1
}
}
write.csv(logFile, file = store, row.names = FALSE)
message("Log file saved: ", store, "\n")
}
return(final.df)
}
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MetReportNames <-
function (data, AmdisReport, base.peak = FALSE, save = TRUE, folder, output = "metab_data", TimeWindow = 2.5, Remove)
{
######################################################
############# Function to check if file is CDF #######
######################################################
isCDFdlg <- function(titleMSG, errorMSG) {
t = 0
while (t == 0) {
checkIfCDF <- dlgOpen(title = titleMSG, multiple = FALSE)$res
checkIfCDF2 <- basename(checkIfCDF)
checkIfCDF3 <- unlist(strsplit(checkIfCDF2, "\\."))
checkIfCDF4 <- checkIfCDF3[length(checkIfCDF3)]
if (checkIfCDF4 %in% c("CDF", "cdf")) {
t = 1
return(checkIfCDF)
} else {
dlgMessage(errorMSG)
}
}
}
#######################################################
################# Check if CDF - No dialog box ########
#######################################################
isCDF <- function(pathFile, errorMSG) {
t = 0
checkIfCDF <- pathFile
checkIfCDF2 <- basename(checkIfCDF)
checkIfCDF3 <- unlist(strsplit(checkIfCDF2, "\\."))
checkIfCDF4 <- checkIfCDF3[length(checkIfCDF3)]
if (checkIfCDF4 %in% c("CDF", "cdf")) {
t = 1
return(t)
} else {
#dlgMessage(errorMSG)
return(t)
}
}
######### Check if a CSV or .msl file ############
isCSVORmsldlg <- function(titleMSG, errorMSG){
t = 0
while (t == 0){
checkIfCsv <- dlgOpen(title = titleMSG, multiple = FALSE)$res
checkIfCsv2 <- basename(checkIfCsv)
checkIfCsv3 <- unlist(strsplit(checkIfCsv2, "\\."))
checkIfCsv4 <- checkIfCsv3[length(checkIfCsv3)]
if (checkIfCsv4 %in% c("CSV", "csv")){
t = 1
return(c(checkIfCsv, "csv"))
} else {
if (checkIfCsv4 %in% c("MSL", "msl")){
t = 1
return(c(checkIfCsv, "msl"))
} else {
dlgMessage(errorMSG)
}
}
}
}
####################################################
######### Check if a CSV or .msl file NO DIALOG BOX ############
isCSVORmsl <- function(pathfile, errorMSG){
t = 0
checkIfCsv2 <- basename(pathfile)
checkIfCsv3 <- unlist(strsplit(checkIfCsv2, "\\."))
checkIfCsv4 <- checkIfCsv3[length(checkIfCsv3)]
if (checkIfCsv4 %in% c("CSV", "csv")){
t = "csv"
return(t)
} else {
if (checkIfCsv4 %in% c("MSL", "msl")){
t = "msl"
return(t)
} else {
t = 0
return(t)
}
}
}
####################################################
##### If no AMDIS report specified ####
if (missing(AmdisReport)) {
AmdisReport <- dlgOpen(title = "Select the AMDIS report generated in batch mode")$res
AmdisReportUsed <- AmdisReport
AmdisReport = read.csv(AmdisReport, sep = "\t", colClass = "character")
} else {
if (is.data.frame(AmdisReport)) {
AmdisReportUsed <- "data_frame"
AmdisReport <- AmdisReport
message("AmdisReport - Data frame loaded...")
} else {
if (is.character(AmdisReport)) {
inputTest <- file.access(AmdisReport, 0)
if (inputTest == 0) {
AmdisReportUsed <- AmdisReport
AmdisReport = read.csv(AmdisReport, sep = "\t", colClasses = "character")
} else {
dlgMessage("The AmdisReport specified is not accessible. Please, select the AMDIS report generated in batch mode.")
AmdisReport <- dlgOpen(title = "Select the AMDIS report generated in batch mode")$res
AmdisReportUsed <- AmdisReport
AmdisReport = read.csv(AmdisReport, sep = "\t", colClass = "character")
}
} else {
dlgMessage("The AmdisReport specified is not valid. Please, select the AMDIS report generated in batch mode.")
AmdisReport <- dlgOpen(title = "Select the AMDIS report generated in batch mode")$res
AmdisReportUsed <- AmdisReport
AmdisReport = read.csv(AmdisReport, sep = "\t", colClass = "character")
}
}
}
total_report <- AmdisReport
if (missing(Remove)){
RemoveUsed <- "None"
} else {
RemoveUsed <- Remove
for (i in 1:length(Remove)){
toRemove <- grep(Remove[i], total_report$Name, ignore.case = FALSE, value = TRUE)
total_report <- subset(total_report, !(total_report$Name %in% toRemove))
}
}
######################################################
########## Collect Data ##############################
######################################################
if (missing(data)) {
filesToAnalyse <- total_report[1]
filesToAnalyse <- data.frame(filesToAnalyse[!duplicated(filesToAnalyse),], stringsAsFactors = FALSE)
filesToAnalyse <- data.frame(gsub("\\", "/", filesToAnalyse[,1], fixed = TRUE), stringsAsFactors = FALSE)
filesToAnalyse <- data.frame(apply(filesToAnalyse, 1, function(x) basename(as.character(x))), stringsAsFactors = FALSE)
filesToAnalyse[1] <- gsub(".FIN", "", filesToAnalyse[,1], fixed = TRUE)
data <- dlgList(filesToAnalyse[,1], multiple = TRUE, title = "Select the files to be analyzed.")$res
dataUsed <- data
} else {
if (is.character(data)) {
dataUsed <- data
dataUsed <- gsub(".FIN", "", dataUsed, fixed = TRUE)
} else {
message("data must be specified as character.")
filesToAnalyse <- total_report[1]
filesToAnalyse <- data.frame(filesToAnalyse[!duplicated(filesToAnalyse),], stringsAsFactors = FALSE)
filesToAnalyse <- data.frame(gsub("\\", "/", filesToAnalyse[,1], fixed = TRUE), stringsAsFactors = FALSE)
filesToAnalyse <- data.frame(apply(filesToAnalyse, 1, function(x) basename(as.character(x))), stringsAsFactors = FALSE)
filesToAnalyse[1] <- gsub(".FIN", "", filesToAnalyse[,1], fixed = TRUE)
data <- dlgList(filesToAnalyse[,1], multiple = TRUE, title = "Select the files to be analyzed.")$res
dataUsed <- data
}
}
######################################################
########## Collect Folder ############################
######################################################
if (save) {
if (missing(folder)) {
folder = dlgDir(title = "Select the folder where the output file will be saved.")$res
} else {
if (is.character(folder)) {
isFolder <- file.access(as.character(folder), 0)
if (isFolder == 0) {
isFolder <- file.info(folder)
if (!isFolder$isdir) {
folder = dlgDir(title = "Select the folder where the output file will be saved.")$res
}
} else {
folder = dlgDir(title = "Select the folder where the output file will be saved.")$res
}
} else {
folder = dlgDir(title = "Select the folder where the output file will be saved.")$res
}
}
}
#################################
###### Start analysis ###########
#################################
Result.df <- 1
for (i in 1:length(dataUsed)){
surefinal <- c()
file <- dataUsed[i]
name.file <- file
file <- paste(file, ".FIN", sep = "")
file <- grep(file, total_report$FileName, fixed = TRUE)
if (length(file) > 0) {
data.df <- total_report[file, ]
if (base.peak){
Keep <- c("Name", "RT", "Scan", "Expec..RT",
"Base.Peak")
AbundancesUsed <- "Base.Peak"
} else {
Keep <- c("Name", "RT", "Scan", "Expec..RT",
"Area")
AbundancesUsed <- "Area"
}
data.df <- data.df[, Keep]
data.df[2] <- as.numeric(data.df[,2])
data.df[3] <- as.numeric(data.df[,3])
data.df[4] <- as.numeric(data.df[,4])
data.df[5] <- as.numeric(data.df[,5])
data.df$deff <- data.df$RT - data.df$Expec..RT
data.df <- subset(data.df, data.df$deff < TimeWindow & data.df$deff > -TimeWindow)
while (nrow(data.df) != 0) {
line <- data.df[1, ]
sameRT <- subset(data.df, data.df$RT == line$RT)
data.df <- data.df[-which(row.names(data.df) %in% row.names(sameRT)),]
if (nrow(sameRT) > 1) {
doub <- grep("[?]", sameRT$Name, value = TRUE)
if (nrow(sameRT) == length(doub)) {
oneq <- grep("^?\\s", sameRT$Name, value = TRUE)
twoq <- grep("^??\\s", sameRT$Name, value = TRUE)
thrq <- grep("^???\\s", sameRT$Name, value = TRUE)
if (length(oneq) == 0) {
if (length(twoq) == 0) {
findCloser <- sameRT
findCloser$deff <- abs(findCloser$deff)
sure <- sameRT[which(findCloser$deff == min(findCloser$deff)),]
if (nrow(sure) > 1){
sure <- sameRT[which(sure$Base.Peak == max(sure$Base.Peak)),]
}
} else {
if (length(twoq) > 1) {
sameRT <- subset(sameRT, sameRT$Name %in% twoq)
findCloser <- sameRT
findCloser$deff <- abs(findCloser$deff)
sure <- sameRT[which(findCloser$deff == min(findCloser$deff)),]
if (nrow(sure) > 1){
sure <- sameRT[which(sure$Base.Peak == max(sure$Base.Peak)),]
}
} else {
sameRT <- subset(sameRT, sameRT$Name %in% twoq)
sure <- sameRT
}
}
} else {
if (length(oneq) > 1){
sameRT <- subset(sameRT, (sameRT$Name %in% oneq))
findCloser <- sameRT
findCloser$deff <- abs(findCloser$deff)
sure <- sameRT[which(findCloser$deff == min(findCloser$deff)),]
if (nrow(sure) > 1){
sure <- sameRT[which(sure$Base.Peak == max(sure$Base.Peak)),]
}
} else {
sameRT <- subset(sameRT, sameRT$Name %in% twoq)
sure <- sameRT
}
}
} else {
sameRT <- subset(sameRT, !(sameRT$Name %in% doub))
if (nrow(sameRT) > 1) {
findCloser <- sameRT
findCloser$deff <- abs(findCloser$deff)
sure <- sameRT[which(findCloser$deff == min(findCloser$deff)),]
if (nrow(sure) > 1){
preSure <- sameRT[which(sure$Base.Peak == max(sure$Base.Peak)),]
sure <- preSure[1,]
}
}
}
} else {
sure <- sameRT
}
if (length(surefinal) == 0){
surefinal <- sure
} else {
surefinal <- rbind(sure, surefinal)
}
}
surefinal <- surefinal[!duplicated(surefinal$RT),]
surefinal[1] <- gsub("? ", "", surefinal[,1], fixed = TRUE)
surefinal[1] <- gsub("?", "", surefinal[,1], fixed = TRUE)
names(surefinal)[5] <- name.file
dupli <- surefinal[duplicated(surefinal[,1]),]
if (nrow(dupli) > 0){
while(nrow(dupli) > 0){
checkDupli <- dupli[1,]
sameName <- subset(surefinal, surefinal$Name == checkDupli$Name)
sameName$deff <- abs(sameName$deff)
choseName <- sameName[which(sameName$deff == min(abs(sameName$deff), na.rm = TRUE)),]
if (nrow(choseName) > 1){
choseName <- choseName[which(choseName[,5] == max(choseName[,5], na.rm = TRUE)),]
}
sameName <- sameName[-(which(row.names(sameName) == row.names(choseName))),]
surefinal <- surefinal[-which(row.names(surefinal) %in% row.names(sameName)),]
dupli <- dupli[-(which(dupli$Name %in% checkDupli$Name)),]
}
}
if (Result.df == 1) {
final.df <- surefinal[c(1,5)]
confirmation <- paste("File", name.file, "done!", sep = " ")
message(confirmation)
Result.df <- Result.df + 1
} else {
surefinal <- surefinal[c(1,5)]
final.df <- merge(final.df, surefinal, by.x = "Name", by.y = "Name", all = TRUE)
confirmation <- paste("File", name.file, "done!", sep = " ")
message(confirmation)
}
} else {
confirmation <- paste("File ", name.file, " not analyzed! Probably there is no metabolites detected for this sample in the AMDIS report", sep = "")
message(confirmation)
final.df$error <- NA
names(final.df)[ncol(final.df)] <- name.file
}
}
final.df <- final.df[order(final.df[, 1], decreasing = F),]
if (save) {
sheet <- output
store <- file.path(folder, paste(sheet, ".csv", sep = ""))
inputTest <- file.access(store, 0)
if (inputTest == 0) {
addFile <- 1
while(inputTest == 0){
store <- file.path(folder, paste(sheet, addFile, ".csv", sep = ""))
inputTest <- file.access(store, 0)
addFile <- addFile + 1
}
}
write.csv(final.df, file = store, row.names = FALSE)
message("File saved: ", store, "\n")
##### Generate log file ######
logFile <- data.frame(Directory = data, Amdis_report = AmdisReportUsed, Output_file = store, Time_window = TimeWindow, Analysis_date = date(), Metabolites_removed = RemoveUsed, Abundances = AbundancesUsed)
sheet <- "logFile"
store <- file.path(folder, paste(sheet, ".csv", sep = ""))
inputTest <- file.access(store, 0)
if (inputTest == 0) {
addFile <- 1
while(inputTest == 0){
store <- file.path(folder, paste(sheet, addFile, ".csv", sep = ""))
inputTest <- file.access(store, 0)
addFile <- addFile + 1
}
}
write.csv(logFile, file = store, row.names = FALSE)
message("Log file saved: ", store, "\n")
}
return(final.df)
}
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