R/fromZtoS.R
In jaspershen/metIdentify: Metabolite identification based on MS1 and MS2 spectra
# setwd("D:/study/database and library/zhu_nist")
# load("zhuMetlib.rda")
#
# info <- zhuMetlib$meta$compound
#
# colnames(info) <- c("Lab.ID", "Compound.name", "mz", "Formula", "CAS.ID", "HMDB.ID")
#
# RT <- rep(NA, nrow(info))
#
# info <- data.frame(info, RT, stringsAsFactors = FALSE)
#
# info$mz <- as.numeric(info$mz)
#
# KEGG.ID <- rep(NA, nrow(info))
#
# info <- data.frame(info, KEGG.ID, stringsAsFactors = FALSE)
#
# info <- info[,c("Lab.ID", "Compound.name", "mz", "RT", "CAS.ID", "HMDB.ID", "KEGG.ID", "Formula")]
#
#
# spectra.pos <- zhuMetlib$compound$pos
# spectra.neg <- zhuMetlib$compound$neg
#
# Spectra <- list("Spectra.positive" = spectra.pos,
# "Spectra.negative" = spectra.neg)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "NIST",
# "Link" = "https://www.nist.gov/srd/national-standard-reference-data-series",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# nistDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = info,
# spectra.data = Spectra)
#
# save(nistDatabase0.0.1, file = 'nistDatabase0.0.1', compress = "xz")
#
#
#
#
#
#
#
# setwd("D:/study/database and library/HMDB")
# load("hmdbLib.rda")
#
# info <- hmdbLib$meta$compound
#
# colnames(info) <- c("Lab.ID", "Compound.name", "mz", "Formula", "CAS.ID", "HMDB.ID",
# "SMILES", "ChemSpider.ID", "METLIN.ID", "KEGG.ID", "SMPDB.ID", "Instrument", "CE", "InChikey")
# info <- info[,-c(11)]
# RT <- rep(NA, nrow(info))
#
# info <- data.frame(info, RT, stringsAsFactors = FALSE)
# info <- info[,c("Lab.ID", "Compound.name", "mz", "RT", "CAS.ID", "HMDB.ID", "KEGG.ID", "Formula", "SMILES",
# "ChemSpider.ID", "METLIN.ID", "Instrument", "CE", "InChikey")]
# info$mz <- as.numeric(info$mz)
#
# metabolite.name <- apply(info[,-c(1, 13)], 1, function(x){
# x <- as.character(x)
# x <- stringr::str_trim(x)
# paste(x, collapse = ";")
# })
#
# unique.metabolite.name <- unique(metabolite.name)
#
# ce <- info$CE
# ce2 <- lapply(unique.metabolite.name, function(x){
# temp.idx <- which(metabolite.name == x)
# temp.ce <- ce[temp.idx]
# if(any(is.na(temp.ce))){
# temp.ce[is.na(temp.ce)] <- paste("Unknown", 1:length(temp.ce[is.na(temp.ce)]), sep = "_")
# # ce[temp.idx] <- temp.ce
# }
# temp.ce
# })
#
#
# temp.idx <- lapply(unique.metabolite.name, function(x){
# temp.idx <- which(metabolite.name == x)
# unname(temp.idx)
# })
#
# for(i in 1:length(temp.idx)){
# ce[temp.idx[[i]]] <- ce2[[i]]
# }
#
#
# cbind(ce, info$CE)
#
#
# info$CE <- ce
#
#
# # info <- info[!duplicated(info[,-1]),]
#
# spectra.pos <- hmdbLib$compound$pos
# spectra.neg <- hmdbLib$compound$neg
#
#
# lab.id <- lapply(unique.metabolite.name, function(x){
# info$Lab.ID[which(x == metabolite.name)]
# })
#
#
# spectra.pos2 <- lapply(lab.id, function(x){
# idx <- match(x, names(spectra.pos))
# if(all(is.na(idx))) return(NA)
# # idx <- idx[!is.na(idx)]
# temp.spec <- spectra.pos[idx]
# temp.spec <- lapply(temp.spec, function(x)x[[1]])
# names(temp.spec) <- info$CE[match(x, info$Lab.ID)]
# temp.spec <- temp.spec[unlist(lapply(temp.spec, function(x) !is.null(x)))]
# temp.spec
# })
#
# spectra.neg2 <- lapply(lab.id, function(x){
# idx <- match(x, names(spectra.neg))
# if(all(is.na(idx))) return(NA)
# # idx <- idx[!is.na(idx)]
# temp.spec <- spectra.neg[idx]
# temp.spec <- lapply(temp.spec, function(x)x[[1]])
# names(temp.spec) <- info$CE[match(x, info$Lab.ID)]
# temp.spec <- temp.spec[unlist(lapply(temp.spec, function(x) !is.null(x)))]
# temp.spec
# })
#
#
# info <- info[!duplicated(info[,-c(1,13)]),]
# info <- info[,-c(13)]
#
#
# metabolite.name2 <- apply(info[,-c(1)], 1, function(x){
# x <- as.character(x)
# x <- stringr::str_trim(x)
# paste(x, collapse = ";")
# })
#
# sum(metabolite.name2 == unique.metabolite.name)
#
# # info$Lab.ID <- paste("shen", paste(info$HMDB.ID, info$Instrument, sep = "_"), sep = "_")
# info$Lab.ID <- paste(paste("shen", 1:nrow(info), sep = "_"), info$HMDB.ID, sep = "_")
#
# names(spectra.pos2) <- names(spectra.neg2) <- info$Lab.ID
#
#
#
# spectra.pos2 <- spectra.pos2[which(!unlist(lapply(spectra.pos2, function(x)all(is.na(x)))))]
# spectra.neg2 <- spectra.neg2[which(!unlist(lapply(spectra.neg2, function(x)all(is.na(x)))))]
#
#
# spectra.pos3 <- lapply(spectra.pos2, function(x){
# x <- lapply(x, function(y){
# y$mz <- as.numeric(y$mz)
# y$intensity <- as.numeric(y$intensity)
# y
# })
# x
# })
#
# spectra.neg3 <- lapply(spectra.neg2, function(x){
# x <- lapply(x, function(y){
# y$mz <- as.numeric(y$mz)
# y$intensity <- as.numeric(y$intensity)
# y
# })
# x
# })
#
#
# Spectra <- list("Spectra.positive" = spectra.pos3,
# "Spectra.negative" = spectra.neg3)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "HMDB",
# "Link" = "http://www.hmdb.ca/",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# hmdbDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = info,
# spectra.data = Spectra)
#
# save(hmdbDatabase0.0.1, file = 'hmdbDatabase0.0.1', compress = "xz")
#
#
#
#
# ####METLIN database
# setwd("D:/study/database and library/metlin")
# load("metlinlib.rdata")
# metlinlib <- metlinlib$v1.0.1710
#
# info <- metlinlib$meta$compound
#
# colnames(info) <- c("Lab.ID", "Compound.name", "mz", "Formula", "HMDB.ID",
# "KEGG.ID", "METLIN.ID", "CAS.ID")
#
# RT <- rep(NA, nrow(info))
#
# info <- data.frame(info, RT, stringsAsFactors = FALSE)
# info <- info[,c("Lab.ID", "Compound.name", "mz", "RT", "CAS.ID", "HMDB.ID", "KEGG.ID", "Formula",
# "METLIN.ID")]
# info$mz <- as.numeric(info$mz)
#
#
#
#
#
#
# spectra.pos <- metlinlib$compound$pos
# spectra.neg <- metlinlib$compound$neg
#
# Spectra <- list("Spectra.positive" = spectra.pos,
# "Spectra.negative" = spectra.neg)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "METLIN",
# "Link" = "https://metlin.scripps.edu/landing_page.php?pgcontent=mainPage",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# metlinDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = info,
# spectra.data = Spectra)
#
# save(metlinDatabase0.0.1, file = 'metlinDatabase0.0.1', compress = "xz")
#
#
#
# ###orbitrap
# setwd("D:/study/database and library/nist_orbitrap")
# load("orbitrapMetlib.rda")
#
#
#
#
#
# info <- orbitrapMetlib$meta$compound
#
# hmdbDatabase0.0.1@spectra.info$HMDB.ID[match(info$cas, hmdbDatabase0.0.1@spectra.info$CAS.ID)]
#
# colnames(info) <- c("Lab.ID", "Compound.name", "mz", "Formula", "CAS.ID", "HMDB.ID")
#
# load("D:/study/database and library/HMDB/hmdbAllinf.rda")
#
# hmdb.id <- cbind(as.character(hmdbAllinf$HMDBID[match(info$CAS.ID, hmdbAllinf$CAS_Registry_Number)]),
# info$HMDB.ID)
#
#
# hmdb.id <- apply(hmdb.id, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# info$hmdb <- hmdb.id
#
# KEGG.ID <- as.character(hmdbAllinf$KEGGID[match(info$CAS.ID, hmdbAllinf$CAS_Registry_Number)])
# KEGG.ID[is.na(KEGG.ID)] <- ""
# KEGG.ID[KEGG.ID == "\t C01586"] <- "C01586"
# KEGG.ID[KEGG.ID == ""] <- NA
#
# RT <- rep(NA, nrow(info))
#
# info <- data.frame(info, RT, KEGG.ID, stringsAsFactors = FALSE)
# info <- info[,c("Lab.ID", "Compound.name", "mz", "RT", "CAS.ID", "HMDB.ID", "KEGG.ID", "Formula")]
# info$mz <- as.numeric(info$mz)
#
#
#
# spectra.pos <- orbitrapMetlib$compound$pos
# spectra.neg <- orbitrapMetlib$compound$neg
#
# Spectra <- list("Spectra.positive" = spectra.pos,
# "Spectra.negative" = spectra.neg)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "NIST",
# "Link" = "https://www.nist.gov/",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# orbitrapDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = info,
# spectra.data = Spectra)
#
# save(orbitrapDatabase0.0.1, file = 'orbitrapDatabase0.0.1', compress = "xz")
#
#
#
# ###massbank
# setwd("D:/study/database and library/MassBank")
# # load("massbank.rdata")
# load("D:/my github/metTools/data/massBankLib.rda")
#
# info <- massBankLib$meta$compound
#
# colnames(info) <- c("Lab.ID", "Compound.name", "mz", "Formula", "CAS.ID", "HMDB.ID",
# "SMILES","IUPAC", "Pubchem.ID","ChemSpider.ID", "Instrument.type",
# "Instrument", "CE", "Adduct", "Precursor.mz")
# info <- info[,-c(14,15)]
#
# RT <- rep(NA, nrow(info))
# KEGG.ID <- as.character(hmdbAllinf$KEGGID[match(info$CAS.ID, hmdbAllinf$CAS_Registry_Number)])
# info <- data.frame(info, RT, KEGG.ID, stringsAsFactors = FALSE)
# info <- info[,c("Lab.ID", "Compound.name", "mz", "RT", "CAS.ID", "HMDB.ID", "KEGG.ID", "Formula", "SMILES",
# "ChemSpider.ID", "Instrument", "Instrument.type", "CE", "IUPAC", "Pubchem.ID")]
#
#
#
# info$mz <- as.numeric(info$mz)
#
# info$CE <- stringr::str_replace(string = info$CE, pattern = "eV", replacement = "")
# info$CE <- stringr::str_replace(string = info$CE, pattern = "V", replacement = "")
# info$CE <- stringr::str_trim(info$CE)
#
#
#
# metabolite.name <- apply(info[,-c(1, 13)], 1, function(x){
# x <- as.character(x)
# x <- stringr::str_trim(x)
# paste(x, collapse = ";")
# })
#
# unique.metabolite.name <- unique(metabolite.name)
#
# ce <- info$CE
# ce2 <- lapply(unique.metabolite.name, function(x){
# temp.idx <- which(metabolite.name == x)
# temp.ce <- ce[temp.idx]
# if(any(is.na(temp.ce))){
# temp.ce[is.na(temp.ce)] <- paste("Unknown", 1:length(temp.ce[is.na(temp.ce)]), sep = "_")
# # ce[temp.idx] <- temp.ce
# }
# temp.ce
# })
#
#
# temp.idx <- lapply(unique.metabolite.name, function(x){
# temp.idx <- which(metabolite.name == x)
# unname(temp.idx)
# })
#
# for(i in 1:length(temp.idx)){
# ce[temp.idx[[i]]] <- ce2[[i]]
# }
#
#
# cbind(ce, info$CE)
#
#
# info$CE <- ce
#
#
# # info <- info[!duplicated(info[,-1]),]
#
# spectra.pos <- massBankLib$compound$pos
# spectra.neg <- massBankLib$compound$neg
#
#
# lab.id <- lapply(unique.metabolite.name, function(x){
# info$Lab.ID[which(x == metabolite.name)]
# })
#
#
# spectra.pos2 <- lapply(lab.id, function(x){
# idx <- match(x, names(spectra.pos))
# if(all(is.na(idx))) return(NA)
# # idx <- idx[!is.na(idx)]
# temp.spec <- spectra.pos[idx]
# temp.spec <- lapply(temp.spec, function(x)x[[1]])
# names(temp.spec) <- info$CE[match(x, info$Lab.ID)]
# temp.spec <- temp.spec[unlist(lapply(temp.spec, function(x) !is.null(x)))]
# temp.spec
# })
#
# spectra.neg2 <- lapply(lab.id, function(x){
# idx <- match(x, names(spectra.neg))
# if(all(is.na(idx))) return(NA)
# # idx <- idx[!is.na(idx)]
# temp.spec <- spectra.neg[idx]
# temp.spec <- lapply(temp.spec, function(x)x[[1]])
# names(temp.spec) <- info$CE[match(x, info$Lab.ID)]
# temp.spec <- temp.spec[unlist(lapply(temp.spec, function(x) !is.null(x)))]
# temp.spec
# })
#
#
# info2 <- info[!duplicated(info[,-c(1,13)]),]
# info2 <- info2[,-c(13)]
#
#
# metabolite.name2 <- apply(info2[,-c(1)], 1, function(x){
# x <- as.character(x)
# x <- stringr::str_trim(x)
# paste(x, collapse = ";")
# })
#
# info2 <- info2[-54,]
# metabolite.name2 <- metabolite.name2[-54]
#
# match(metabolite.name2, unique.metabolite.name)
# setdiff(metabolite.name2, unique.metabolite.name)
# setdiff(unique.metabolite.name,metabolite.name2)
# # intersect(metabolite.name2, unique.metabolite.name)
#
# sum(metabolite.name2 == unique.metabolite.name)
#
# # info$Lab.ID <- paste("shen", paste(info$HMDB.ID, info$Instrument, sep = "_"), sep = "_")
# info <- info2
# info$Lab.ID <- paste("MassBank", 1:nrow(info), sep = "_")
#
# names(spectra.pos2) <- names(spectra.neg2) <- info$Lab.ID
#
#
#
# spectra.pos2 <- spectra.pos2[which(!unlist(lapply(spectra.pos2, function(x)all(is.na(x)))))]
# spectra.neg2 <- spectra.neg2[which(!unlist(lapply(spectra.neg2, function(x)all(is.na(x)))))]
#
#
# spectra.pos3 <- lapply(spectra.pos2, function(x){
# x <- lapply(x, function(y){
# y$mz <- as.numeric(y$mz)
# y$intensity <- as.numeric(y$intensity)
# y
# })
# x
# })
#
# spectra.neg3 <- lapply(spectra.neg2, function(x){
# x <- lapply(x, function(y){
# y$mz <- as.numeric(y$mz)
# y$intensity <- as.numeric(y$intensity)
# y
# })
# x
# })
#
#
# Spectra <- list("Spectra.positive" = spectra.pos3,
# "Spectra.negative" = spectra.neg3)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "MassBank",
# "Link" = "http://www.massbank.jp/",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# massbankDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = info,
# spectra.data = Spectra)
#
# save(massbankDatabase0.0.1, file = 'massbankDatabase0.0.1', compress = "xz")
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
# ###massbank
# setwd("D:/study/database and library/MoNA")
# # load("massbank.rdata")
# load("D:/my github/metTools/data/monaLib.rda")
# load("mona_spec")
# info <- lapply(mona_spec, function(x) x[[1]])
#
# comment <- unlist(pbapply::pblapply(info, function(x){
# as.character(x["Comments", 1])
# }))
#
#
# which(unlist(pbapply::pblapply(comment, function(x){
# length(grep(pattern = "\\[c16h15n7-h\\]\\+", x = x)) > 0
# })))
#
#
# comment <- pbapply::pblapply(comment, function(x){
# x <- stringr::str_split(string = x, pattern = "\\\"")[[1]]
# x <- x[which(x != "" & x != " ")]
# temp.idx <- grep("theoretical m/z", x)
# if(length(temp.idx) > 0){
# x <- x[-temp.idx]
# }
# x
# })
#
# comment2 <- pbapply::pblapply(comment, function(x){
# x <- stringr::str_split(string = x, pattern = "=", n = 2)
# x <- do.call(rbind, x)
# colnames(x) <- c("Item", "Value")
# x
# })
#
# load('comment2')
# item.list <- unique(unlist(pbapply::pblapply(comment2, function(x){
# x[,1]
# })))
#
# item.list <- item.list[-grep("\\+", item.list)]
#
# item.list <- item.list[item.list %in% c("SMILES", "cas", "pubchem cid", "chemspider", "InChI", "accession", "exact mass", "submitter",
# "kegg", "chebi", "pubchem", "lipidmaps", "compound class", "lipidbank", "scientific name",
# "hmdb", "pubchem sid", "ionization energy", "ion type", "ms type", "ion mode", "fragment voltage",
# "cas number", "pubmed id", "adduct", "exactmass", "synonym", "PubChem", "collision energy spread",
# "formula", "accurate mass", "adduct ion name", "species", "collision energy voltage", "collision energy level",
# "smiles", "compound id", "instrumenttype", "nomralized collision energy")]
#
#
# rm(list = "comment2")
# # for(i in 123788:length(comment2)){
# # cat(i, " ")
# # x <- comment2[[i]]
# # temp <- data.frame("Item" = item.list, "Value" = NA, stringsAsFactors = FALSE)
# # x <- x[x[,1] %in% temp$Item,, drop = FALSE]
# # temp[match(x[,1], temp[,1]),] <- x
# # temp <- as.data.frame(t(temp))
# # temp <- temp[2,,drop = FALSE]
# # # temp
# # }
#
# # for(i in 1:nrow())
#
#
# comment3 <- pbapply::pblapply(comment2, function(x){
# temp <- data.frame("Item" = item.list, "Value" = NA, stringsAsFactors = FALSE)
# x <- x[x[,1] %in% temp$Item,, drop = FALSE]
# temp[match(x[,1], temp[,1]),] <- x
# temp <- as.data.frame(t(temp))
# temp <- temp[2,,drop = FALSE]
# temp
# })
#
#
# save(comment3, file = "comment3")
# rm(list = "comment2")
#
#
# comment4 <- pbapply::pblapply(comment3, function(x){
# x <- apply(x, 1, as.character)[,1,drop = TRUE]
# x
# })
#
# rm(list = "comment3")
#
#
# comment5 <- do.call(rbind, comment4)
#
# colnames(comment5) <- item.list
#
# save(comment5, file = "comment5")
# rm(list = "comment4")
# load("mona_spec")
#
# spectra.data <- pbapply::pblapply(mona_spec, function(x){
# x[[2]]
# })
#
# rm(list = "mona_spec")
#
# info <- pbapply::pblapply(mona_spec, function(x){
# x <- x[[1]]
# x <- x[which(!rownames(x) %in% c("Comments", "Num Peaks")),]
# })
#
# item.list2 <- unique(unlist(pbapply::pblapply(info, function(x){
# rownames(x)
# })))
#
# item.list2 <- item.list2[item.list2 %in% c("Name", "Synon", "InChIKey", "Precursor_type", "Spectrum_type",
# "Instrument_type", "Instrument", "Ion_mode",
# "Collision_energy", "Formula", "ExactMass")]
#
#
#
#
#
# info <- pbapply::pblapply(info, function(x){
# temp <- data.frame("Item" = item.list2, "Value" = NA, stringsAsFactors = FALSE)
# x <- x[rownames(x) %in% temp$Item,, drop = FALSE]
# temp[match(rownames(x), temp[,1]),2] <- x[,1]
# temp <- as.data.frame(t(temp), stringsAsFactors = FALSE)
# temp <- temp[2,,drop = FALSE]
# temp
# })
#
# info <- do.call(rbind, info)
#
# colnames(info) <- item.list2
#
#
# info <- cbind(info, comment5)
#
# rm(list = "comment5")
# save(info, file = "info")
# load("info")
# info2 <- t(apply(info, 1, as.character))
# colnames(info2) <- colnames(info)
#
# rm(list = "info")
#
# info2 <- as.data.frame(info2, stringsAsFactors = FALSE)
#
# ###remove some spectra
# ##Not MS2 spectrum
# spectrum.type <- info2$Spectrum_type
# spectrum.type[is.na(spectrum.type)] <- ""
# remove.idx <- which(info2$Spectrum_type %in% c("MS", "MS1", "MS3", 'MS4'))
# info2 <- info2[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
# ##No polarity
# polarity <- info2[,c("Ion_mode", "ion mode")]
# polarity <- apply(polarity, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# remove.idx <- which(is.na(polarity))
# info2 <- info2[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
#
# ###nature product
# class <- info2$`compound class`
# class[is.na(class)] <- ""
#
# remove.idx <- grep("Natural Product", class, value = FALSE)
# info2 <- info2[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
#
# Compound.name <- info2$Name
# sum(is.na(Compound.name))
#
# Compound.name <- info2$Name
# sum(is.na(Compound.name))
#
# Synonym <- info2$Synon
# sum(is.na(Synonym))
#
# Spectra.adduct <- info2[,c("Precursor_type", "adduct", "ion type")]
#
# Spectra.adduct <- apply(Spectra.adduct, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# Spectra.type <- info2$Spectrum_type
#
# Instrument.type <- info2[,c("Instrument_type", "instrumenttype")]
# Instrument.type <- apply(Instrument.type, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# Instrument <- info2$Instrument
#
# Polarity <- info2[, c("Ion_mode", "ion mode")]
# Polarity <- apply(Polarity, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# Polarity[Polarity == "P"] <- "Positive"
# Polarity[Polarity == "N"] <- "Negative"
#
# CE <- info2[,c("Collision_energy","collision energy voltage")]
#
# CE <- apply(CE, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# CE <- stringr::str_replace_all(string = CE, pattern = "eV|V", replacement = "")
# CE <- stringr::str_trim(CE)
#
#
# Formula <- info2[,c("Formula", "formula")]
#
# Formula <- apply(Formula, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
#
# mz <- info2[,c("ExactMass", "exactmass", "accurate mass")]
# mz <- apply(mz, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# mz <- as.numeric(mz)
#
# SMILES <- info2[,c("SMILES", "smiles")]
# SMILES <- apply(SMILES, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
#
# CAS.ID <- info2[,c("cas", "cas number")]
#
# CAS.ID <- apply(CAS.ID, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# PubChem.CID <- info2$`pubchem cid`
#
# Chemspider.ID <- info2$chemspider
#
# InChI <- info2$InChI
#
# MoNA.ID <- info2$accession
#
# Submitter <- info2$submitter
#
# KEGG.ID <- info2$kegg
#
# Chebi.ID <- info2$chebi
#
# PubChem.ID <- info2[,c("pubchem", "pubmed id", "PubChem")]
#
# PubChem.ID <- apply(PubChem.ID, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
#
# Lipidmaps.ID <- info2$lipidmaps
#
#
# Compound.class <- info2$`compound class`
#
# Lipidbank.ID <- info2$lipidbank
#
# HMDB.ID <- info2$hmdb
#
# PubChem.SID <- info2$`pubchem sid`
#
#
# InChIKey <- info2$InChIKey
# InChI <- info2$InChI
# Spectra.adduct <- info2$Precursor_type
#
#
# spectra.info <- data.frame(Lab.ID = NA, Compound.name, mz, RT = NA, CAS.ID, HMDB.ID, KEGG.ID, Formula,
# CE, Chebi.ID, Chemspider.ID, Compound.class, InChI, InChIKey, Instrument,
# Instrument.type, Polarity, PubChem.CID, PubChem.ID, PubChem.SID, SMILES,
# Spectra.adduct, Spectra.type, Submitter,
# Synonym,
# stringsAsFactors = FALSE
# )
#
# save(spectra.info, file = "spectra.info")
# save(spectra.data, file = "spectra.data")
# load("spectra.data")
# ##remove some spectrum
# remove.idx <- which(is.na(spectra.info$mz))
#
# spectra.info <- spectra.info[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
# length(spectra.data)
# dim(spectra.info)
#
# remove.idx <- which(is.na(spectra.info$Formula))
#
# spectra.info <- spectra.info[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
# length(spectra.data)
# dim(spectra.info)
#
# remove.idx <- which(is.na(spectra.info$Compound.name))
#
#
# table(spectra.info$Submitter)
#
# remove.idx <- c(grep("(Markus Kohlhoff)|(GNPS Collaboration)|(Arpana Vaniya)", spectra.info$Submitter))
#
# table(spectra.info$Submitter[remove.idx])
#
# spectra.info[grep("Arpana Vaniya", spectra.info$Submitter), "Compound.name"]
#
# spectra.info <- spectra.info[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
# length(spectra.data)
# dim(spectra.info)
#
# ##remove some duplicated spectra
# temp.id <- apply(spectra.info[,c(2, 8, 15, 17, 22, 24, 9)], 1, function(x){
# paste(as.character(x), collapse = ";")
# })
#
# unique.temp.id <- unique(temp.id)
#
# temp.idx <- which(unlist(pbapply::pblapply(unique.temp.id, function(x){
# sum(x == temp.id)
# })) > 1)
#
#
# remove.idx <- which(duplicated(temp.id))
#
# spectra.info <- spectra.info[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
# length(spectra.data)
# dim(spectra.info)
#
#
# # spectra.info$CE <- stringr::str_repla
#
#
#
# Lab.ID1 <- apply(spectra.info[,c(2, 8, 15, 17, 22, 24, 9)], 1, function(x){
# paste(as.character(x), collapse = ";")
# })
#
# Lab.ID2 <- apply(spectra.info[,c(2, 8, 15, 17, 22, 24)], 1, function(x){
# paste(as.character(x), collapse = ";")
# })
#
#
# spectra.info$Lab.ID <- Lab.ID2
#
# names(spectra.data) <- Lab.ID1
#
#
# spectra.pos <- spectra.data[grep("Positive", Lab.ID1)]
# spectra.neg <- spectra.data[grep("Negative", Lab.ID1)]
#
# unique.lab.id.pos <- unique(grep("Positive", Lab.ID2, value = TRUE))
# unique.lab.id.neg <- unique(grep("Negative", Lab.ID2, value = TRUE))
#
#
# spectra.pos.name2 <- grep("Positive", Lab.ID2, value = TRUE)
# spectra.neg.name2 <- grep("Negative", Lab.ID2, value = TRUE)
#
#
# spectra.pos2 <- pbapply::pblapply(unique.lab.id.pos, function(x){
# temp.idx <- which(x == spectra.pos.name2)
# temp.spectra.pos <- spectra.pos[temp.idx]
# temp.ce <- unlist(lapply(stringr::str_split(string = names(temp.spectra.pos), pattern = ";"), function(x){
# tail(x, 1)
# }))
#
# temp.ce[is.na(temp.ce)] <- paste("Unknown", 1:length(temp.ce[is.na(temp.ce)]), sep = "_")
# names(temp.spectra.pos) <- temp.ce
# temp.spectra.pos
# })
#
#
#
# names(spectra.pos2) <- unique.lab.id.pos
#
#
# spectra.neg2 <- pbapply::pblapply(unique.lab.id.neg, function(x){
# temp.idx <- which(x == spectra.neg.name2)
# temp.spectra.neg <- spectra.neg[temp.idx]
# temp.ce <- unlist(lapply(stringr::str_split(string = names(temp.spectra.neg), pattern = ";"), function(x){
# tail(x, 1)
# }))
#
# temp.ce[is.na(temp.ce)] <- paste("Unknown", 1:length(temp.ce[is.na(temp.ce)]), sep = "_")
# names(temp.spectra.neg) <- temp.ce
# temp.spectra.neg
# })
#
#
#
# names(spectra.neg2) <- unique.lab.id.neg
#
#
# ###change ID
# colnames(spectra.info)
# Lab.ID <- spectra.info$Lab.ID
#
# Lab.ID3 <- apply(spectra.info[,c(2, 8, 15, 22, 24)], 1, function(x){
# paste(as.character(x), collapse = ";")
# })
#
#
# remove.idx <- which(duplicated(Lab.ID3))
#
# Lab.ID <- Lab.ID[-remove.idx]
# Lab.ID3 <- Lab.ID3[-remove.idx]
#
# spectra.info2 <- spectra.info[-remove.idx,]
#
# spectra.info2$Lab.ID <- paste("MONA", 1:nrow(spectra.info2), sep = "_")
#
#
# sum(is.na(match(stringr::str_replace(string = names(spectra.pos2), pattern = "Positive;", replacement = ""),
# Lab.ID3)))
#
#
# names(spectra.pos2) <- spectra.info2$Lab.ID[match(stringr::str_replace(string = names(spectra.pos2), pattern = "Positive;", replacement = ""),
# Lab.ID3)]
#
#
# sum(is.na(match(stringr::str_replace(string = names(spectra.neg2), pattern = "Negative;", replacement = ""),
# Lab.ID3)))
#
#
# names(spectra.neg2) <- spectra.info2$Lab.ID[match(stringr::str_replace(string = names(spectra.neg2), pattern = "Negative;", replacement = ""),
# Lab.ID3)]
#
#
# intersect(names(spectra.pos2), names(spectra.neg2))
#
#
# Spectra <- list("Spectra.positive" = spectra.pos2,
# "Spectra.negative" = spectra.neg2)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "MoNA",
# "Link" = "http://mona.fiehnlab.ucdavis.edu/",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# monaDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = spectra.info2,
# spectra.data = Spectra)
#
# save(monaDatabase0.0.1, file = 'monaDatabase0.0.1', compress = "xz")
#
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# setwd("D:/study/database and library/zhu_nist")
# load("zhuMetlib.rda")
#
# info <- zhuMetlib$meta$compound
#
# colnames(info) <- c("Lab.ID", "Compound.name", "mz", "Formula", "CAS.ID", "HMDB.ID")
#
# RT <- rep(NA, nrow(info))
#
# info <- data.frame(info, RT, stringsAsFactors = FALSE)
#
# info$mz <- as.numeric(info$mz)
#
# KEGG.ID <- rep(NA, nrow(info))
#
# info <- data.frame(info, KEGG.ID, stringsAsFactors = FALSE)
#
# info <- info[,c("Lab.ID", "Compound.name", "mz", "RT", "CAS.ID", "HMDB.ID", "KEGG.ID", "Formula")]
#
#
# spectra.pos <- zhuMetlib$compound$pos
# spectra.neg <- zhuMetlib$compound$neg
#
# Spectra <- list("Spectra.positive" = spectra.pos,
# "Spectra.negative" = spectra.neg)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "NIST",
# "Link" = "https://www.nist.gov/srd/national-standard-reference-data-series",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# nistDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = info,
# spectra.data = Spectra)
#
# save(nistDatabase0.0.1, file = 'nistDatabase0.0.1', compress = "xz")
#
#
#
#
#
#
#
# setwd("D:/study/database and library/HMDB")
# load("hmdbLib.rda")
#
# info <- hmdbLib$meta$compound
#
# colnames(info) <- c("Lab.ID", "Compound.name", "mz", "Formula", "CAS.ID", "HMDB.ID",
# "SMILES", "ChemSpider.ID", "METLIN.ID", "KEGG.ID", "SMPDB.ID", "Instrument", "CE", "InChikey")
# info <- info[,-c(11)]
# RT <- rep(NA, nrow(info))
#
# info <- data.frame(info, RT, stringsAsFactors = FALSE)
# info <- info[,c("Lab.ID", "Compound.name", "mz", "RT", "CAS.ID", "HMDB.ID", "KEGG.ID", "Formula", "SMILES",
# "ChemSpider.ID", "METLIN.ID", "Instrument", "CE", "InChikey")]
# info$mz <- as.numeric(info$mz)
#
# metabolite.name <- apply(info[,-c(1, 13)], 1, function(x){
# x <- as.character(x)
# x <- stringr::str_trim(x)
# paste(x, collapse = ";")
# })
#
# unique.metabolite.name <- unique(metabolite.name)
#
# ce <- info$CE
# ce2 <- lapply(unique.metabolite.name, function(x){
# temp.idx <- which(metabolite.name == x)
# temp.ce <- ce[temp.idx]
# if(any(is.na(temp.ce))){
# temp.ce[is.na(temp.ce)] <- paste("Unknown", 1:length(temp.ce[is.na(temp.ce)]), sep = "_")
# # ce[temp.idx] <- temp.ce
# }
# temp.ce
# })
#
#
# temp.idx <- lapply(unique.metabolite.name, function(x){
# temp.idx <- which(metabolite.name == x)
# unname(temp.idx)
# })
#
# for(i in 1:length(temp.idx)){
# ce[temp.idx[[i]]] <- ce2[[i]]
# }
#
#
# cbind(ce, info$CE)
#
#
# info$CE <- ce
#
#
# # info <- info[!duplicated(info[,-1]),]
#
# spectra.pos <- hmdbLib$compound$pos
# spectra.neg <- hmdbLib$compound$neg
#
#
# lab.id <- lapply(unique.metabolite.name, function(x){
# info$Lab.ID[which(x == metabolite.name)]
# })
#
#
# spectra.pos2 <- lapply(lab.id, function(x){
# idx <- match(x, names(spectra.pos))
# if(all(is.na(idx))) return(NA)
# # idx <- idx[!is.na(idx)]
# temp.spec <- spectra.pos[idx]
# temp.spec <- lapply(temp.spec, function(x)x[[1]])
# names(temp.spec) <- info$CE[match(x, info$Lab.ID)]
# temp.spec <- temp.spec[unlist(lapply(temp.spec, function(x) !is.null(x)))]
# temp.spec
# })
#
# spectra.neg2 <- lapply(lab.id, function(x){
# idx <- match(x, names(spectra.neg))
# if(all(is.na(idx))) return(NA)
# # idx <- idx[!is.na(idx)]
# temp.spec <- spectra.neg[idx]
# temp.spec <- lapply(temp.spec, function(x)x[[1]])
# names(temp.spec) <- info$CE[match(x, info$Lab.ID)]
# temp.spec <- temp.spec[unlist(lapply(temp.spec, function(x) !is.null(x)))]
# temp.spec
# })
#
#
# info <- info[!duplicated(info[,-c(1,13)]),]
# info <- info[,-c(13)]
#
#
# metabolite.name2 <- apply(info[,-c(1)], 1, function(x){
# x <- as.character(x)
# x <- stringr::str_trim(x)
# paste(x, collapse = ";")
# })
#
# sum(metabolite.name2 == unique.metabolite.name)
#
# # info$Lab.ID <- paste("shen", paste(info$HMDB.ID, info$Instrument, sep = "_"), sep = "_")
# info$Lab.ID <- paste(paste("shen", 1:nrow(info), sep = "_"), info$HMDB.ID, sep = "_")
#
# names(spectra.pos2) <- names(spectra.neg2) <- info$Lab.ID
#
#
#
# spectra.pos2 <- spectra.pos2[which(!unlist(lapply(spectra.pos2, function(x)all(is.na(x)))))]
# spectra.neg2 <- spectra.neg2[which(!unlist(lapply(spectra.neg2, function(x)all(is.na(x)))))]
#
#
# spectra.pos3 <- lapply(spectra.pos2, function(x){
# x <- lapply(x, function(y){
# y$mz <- as.numeric(y$mz)
# y$intensity <- as.numeric(y$intensity)
# y
# })
# x
# })
#
# spectra.neg3 <- lapply(spectra.neg2, function(x){
# x <- lapply(x, function(y){
# y$mz <- as.numeric(y$mz)
# y$intensity <- as.numeric(y$intensity)
# y
# })
# x
# })
#
#
# Spectra <- list("Spectra.positive" = spectra.pos3,
# "Spectra.negative" = spectra.neg3)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "HMDB",
# "Link" = "http://www.hmdb.ca/",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# hmdbDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = info,
# spectra.data = Spectra)
#
# save(hmdbDatabase0.0.1, file = 'hmdbDatabase0.0.1', compress = "xz")
#
#
#
#
# ####METLIN database
# setwd("D:/study/database and library/metlin")
# load("metlinlib.rdata")
# metlinlib <- metlinlib$v1.0.1710
#
# info <- metlinlib$meta$compound
#
# colnames(info) <- c("Lab.ID", "Compound.name", "mz", "Formula", "HMDB.ID",
# "KEGG.ID", "METLIN.ID", "CAS.ID")
#
# RT <- rep(NA, nrow(info))
#
# info <- data.frame(info, RT, stringsAsFactors = FALSE)
# info <- info[,c("Lab.ID", "Compound.name", "mz", "RT", "CAS.ID", "HMDB.ID", "KEGG.ID", "Formula",
# "METLIN.ID")]
# info$mz <- as.numeric(info$mz)
#
#
#
#
#
#
# spectra.pos <- metlinlib$compound$pos
# spectra.neg <- metlinlib$compound$neg
#
# Spectra <- list("Spectra.positive" = spectra.pos,
# "Spectra.negative" = spectra.neg)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "METLIN",
# "Link" = "https://metlin.scripps.edu/landing_page.php?pgcontent=mainPage",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# metlinDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = info,
# spectra.data = Spectra)
#
# save(metlinDatabase0.0.1, file = 'metlinDatabase0.0.1', compress = "xz")
#
#
#
# ###orbitrap
# setwd("D:/study/database and library/nist_orbitrap")
# load("orbitrapMetlib.rda")
#
#
#
#
#
# info <- orbitrapMetlib$meta$compound
#
# hmdbDatabase0.0.1@spectra.info$HMDB.ID[match(info$cas, hmdbDatabase0.0.1@spectra.info$CAS.ID)]
#
# colnames(info) <- c("Lab.ID", "Compound.name", "mz", "Formula", "CAS.ID", "HMDB.ID")
#
# load("D:/study/database and library/HMDB/hmdbAllinf.rda")
#
# hmdb.id <- cbind(as.character(hmdbAllinf$HMDBID[match(info$CAS.ID, hmdbAllinf$CAS_Registry_Number)]),
# info$HMDB.ID)
#
#
# hmdb.id <- apply(hmdb.id, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# info$hmdb <- hmdb.id
#
# KEGG.ID <- as.character(hmdbAllinf$KEGGID[match(info$CAS.ID, hmdbAllinf$CAS_Registry_Number)])
# KEGG.ID[is.na(KEGG.ID)] <- ""
# KEGG.ID[KEGG.ID == "\t C01586"] <- "C01586"
# KEGG.ID[KEGG.ID == ""] <- NA
#
# RT <- rep(NA, nrow(info))
#
# info <- data.frame(info, RT, KEGG.ID, stringsAsFactors = FALSE)
# info <- info[,c("Lab.ID", "Compound.name", "mz", "RT", "CAS.ID", "HMDB.ID", "KEGG.ID", "Formula")]
# info$mz <- as.numeric(info$mz)
#
#
#
# spectra.pos <- orbitrapMetlib$compound$pos
# spectra.neg <- orbitrapMetlib$compound$neg
#
# Spectra <- list("Spectra.positive" = spectra.pos,
# "Spectra.negative" = spectra.neg)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "NIST",
# "Link" = "https://www.nist.gov/",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# orbitrapDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = info,
# spectra.data = Spectra)
#
# save(orbitrapDatabase0.0.1, file = 'orbitrapDatabase0.0.1', compress = "xz")
#
#
#
# ###massbank
# setwd("D:/study/database and library/MassBank")
# # load("massbank.rdata")
# load("D:/my github/metTools/data/massBankLib.rda")
#
# info <- massBankLib$meta$compound
#
# colnames(info) <- c("Lab.ID", "Compound.name", "mz", "Formula", "CAS.ID", "HMDB.ID",
# "SMILES","IUPAC", "Pubchem.ID","ChemSpider.ID", "Instrument.type",
# "Instrument", "CE", "Adduct", "Precursor.mz")
# info <- info[,-c(14,15)]
#
# RT <- rep(NA, nrow(info))
# KEGG.ID <- as.character(hmdbAllinf$KEGGID[match(info$CAS.ID, hmdbAllinf$CAS_Registry_Number)])
# info <- data.frame(info, RT, KEGG.ID, stringsAsFactors = FALSE)
# info <- info[,c("Lab.ID", "Compound.name", "mz", "RT", "CAS.ID", "HMDB.ID", "KEGG.ID", "Formula", "SMILES",
# "ChemSpider.ID", "Instrument", "Instrument.type", "CE", "IUPAC", "Pubchem.ID")]
#
#
#
# info$mz <- as.numeric(info$mz)
#
# info$CE <- stringr::str_replace(string = info$CE, pattern = "eV", replacement = "")
# info$CE <- stringr::str_replace(string = info$CE, pattern = "V", replacement = "")
# info$CE <- stringr::str_trim(info$CE)
#
#
#
# metabolite.name <- apply(info[,-c(1, 13)], 1, function(x){
# x <- as.character(x)
# x <- stringr::str_trim(x)
# paste(x, collapse = ";")
# })
#
# unique.metabolite.name <- unique(metabolite.name)
#
# ce <- info$CE
# ce2 <- lapply(unique.metabolite.name, function(x){
# temp.idx <- which(metabolite.name == x)
# temp.ce <- ce[temp.idx]
# if(any(is.na(temp.ce))){
# temp.ce[is.na(temp.ce)] <- paste("Unknown", 1:length(temp.ce[is.na(temp.ce)]), sep = "_")
# # ce[temp.idx] <- temp.ce
# }
# temp.ce
# })
#
#
# temp.idx <- lapply(unique.metabolite.name, function(x){
# temp.idx <- which(metabolite.name == x)
# unname(temp.idx)
# })
#
# for(i in 1:length(temp.idx)){
# ce[temp.idx[[i]]] <- ce2[[i]]
# }
#
#
# cbind(ce, info$CE)
#
#
# info$CE <- ce
#
#
# # info <- info[!duplicated(info[,-1]),]
#
# spectra.pos <- massBankLib$compound$pos
# spectra.neg <- massBankLib$compound$neg
#
#
# lab.id <- lapply(unique.metabolite.name, function(x){
# info$Lab.ID[which(x == metabolite.name)]
# })
#
#
# spectra.pos2 <- lapply(lab.id, function(x){
# idx <- match(x, names(spectra.pos))
# if(all(is.na(idx))) return(NA)
# # idx <- idx[!is.na(idx)]
# temp.spec <- spectra.pos[idx]
# temp.spec <- lapply(temp.spec, function(x)x[[1]])
# names(temp.spec) <- info$CE[match(x, info$Lab.ID)]
# temp.spec <- temp.spec[unlist(lapply(temp.spec, function(x) !is.null(x)))]
# temp.spec
# })
#
# spectra.neg2 <- lapply(lab.id, function(x){
# idx <- match(x, names(spectra.neg))
# if(all(is.na(idx))) return(NA)
# # idx <- idx[!is.na(idx)]
# temp.spec <- spectra.neg[idx]
# temp.spec <- lapply(temp.spec, function(x)x[[1]])
# names(temp.spec) <- info$CE[match(x, info$Lab.ID)]
# temp.spec <- temp.spec[unlist(lapply(temp.spec, function(x) !is.null(x)))]
# temp.spec
# })
#
#
# info2 <- info[!duplicated(info[,-c(1,13)]),]
# info2 <- info2[,-c(13)]
#
#
# metabolite.name2 <- apply(info2[,-c(1)], 1, function(x){
# x <- as.character(x)
# x <- stringr::str_trim(x)
# paste(x, collapse = ";")
# })
#
# info2 <- info2[-54,]
# metabolite.name2 <- metabolite.name2[-54]
#
# match(metabolite.name2, unique.metabolite.name)
# setdiff(metabolite.name2, unique.metabolite.name)
# setdiff(unique.metabolite.name,metabolite.name2)
# # intersect(metabolite.name2, unique.metabolite.name)
#
# sum(metabolite.name2 == unique.metabolite.name)
#
# # info$Lab.ID <- paste("shen", paste(info$HMDB.ID, info$Instrument, sep = "_"), sep = "_")
# info <- info2
# info$Lab.ID <- paste("MassBank", 1:nrow(info), sep = "_")
#
# names(spectra.pos2) <- names(spectra.neg2) <- info$Lab.ID
#
#
#
# spectra.pos2 <- spectra.pos2[which(!unlist(lapply(spectra.pos2, function(x)all(is.na(x)))))]
# spectra.neg2 <- spectra.neg2[which(!unlist(lapply(spectra.neg2, function(x)all(is.na(x)))))]
#
#
# spectra.pos3 <- lapply(spectra.pos2, function(x){
# x <- lapply(x, function(y){
# y$mz <- as.numeric(y$mz)
# y$intensity <- as.numeric(y$intensity)
# y
# })
# x
# })
#
# spectra.neg3 <- lapply(spectra.neg2, function(x){
# x <- lapply(x, function(y){
# y$mz <- as.numeric(y$mz)
# y$intensity <- as.numeric(y$intensity)
# y
# })
# x
# })
#
#
# Spectra <- list("Spectra.positive" = spectra.pos3,
# "Spectra.negative" = spectra.neg3)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "MassBank",
# "Link" = "http://www.massbank.jp/",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# massbankDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = info,
# spectra.data = Spectra)
#
# save(massbankDatabase0.0.1, file = 'massbankDatabase0.0.1', compress = "xz")
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
# ###massbank
# setwd("D:/study/database and library/MoNA")
# # load("massbank.rdata")
# load("D:/my github/metTools/data/monaLib.rda")
# load("mona_spec")
# info <- lapply(mona_spec, function(x) x[[1]])
#
# comment <- unlist(pbapply::pblapply(info, function(x){
# as.character(x["Comments", 1])
# }))
#
#
# which(unlist(pbapply::pblapply(comment, function(x){
# length(grep(pattern = "\\[c16h15n7-h\\]\\+", x = x)) > 0
# })))
#
#
# comment <- pbapply::pblapply(comment, function(x){
# x <- stringr::str_split(string = x, pattern = "\\\"")[[1]]
# x <- x[which(x != "" & x != " ")]
# temp.idx <- grep("theoretical m/z", x)
# if(length(temp.idx) > 0){
# x <- x[-temp.idx]
# }
# x
# })
#
# comment2 <- pbapply::pblapply(comment, function(x){
# x <- stringr::str_split(string = x, pattern = "=", n = 2)
# x <- do.call(rbind, x)
# colnames(x) <- c("Item", "Value")
# x
# })
#
# load('comment2')
# item.list <- unique(unlist(pbapply::pblapply(comment2, function(x){
# x[,1]
# })))
#
# item.list <- item.list[-grep("\\+", item.list)]
#
# item.list <- item.list[item.list %in% c("SMILES", "cas", "pubchem cid", "chemspider", "InChI", "accession", "exact mass", "submitter",
# "kegg", "chebi", "pubchem", "lipidmaps", "compound class", "lipidbank", "scientific name",
# "hmdb", "pubchem sid", "ionization energy", "ion type", "ms type", "ion mode", "fragment voltage",
# "cas number", "pubmed id", "adduct", "exactmass", "synonym", "PubChem", "collision energy spread",
# "formula", "accurate mass", "adduct ion name", "species", "collision energy voltage", "collision energy level",
# "smiles", "compound id", "instrumenttype", "nomralized collision energy")]
#
#
# rm(list = "comment2")
# # for(i in 123788:length(comment2)){
# # cat(i, " ")
# # x <- comment2[[i]]
# # temp <- data.frame("Item" = item.list, "Value" = NA, stringsAsFactors = FALSE)
# # x <- x[x[,1] %in% temp$Item,, drop = FALSE]
# # temp[match(x[,1], temp[,1]),] <- x
# # temp <- as.data.frame(t(temp))
# # temp <- temp[2,,drop = FALSE]
# # # temp
# # }
#
# # for(i in 1:nrow())
#
#
# comment3 <- pbapply::pblapply(comment2, function(x){
# temp <- data.frame("Item" = item.list, "Value" = NA, stringsAsFactors = FALSE)
# x <- x[x[,1] %in% temp$Item,, drop = FALSE]
# temp[match(x[,1], temp[,1]),] <- x
# temp <- as.data.frame(t(temp))
# temp <- temp[2,,drop = FALSE]
# temp
# })
#
#
# save(comment3, file = "comment3")
# rm(list = "comment2")
#
#
# comment4 <- pbapply::pblapply(comment3, function(x){
# x <- apply(x, 1, as.character)[,1,drop = TRUE]
# x
# })
#
# rm(list = "comment3")
#
#
# comment5 <- do.call(rbind, comment4)
#
# colnames(comment5) <- item.list
#
# save(comment5, file = "comment5")
# rm(list = "comment4")
# load("mona_spec")
#
# spectra.data <- pbapply::pblapply(mona_spec, function(x){
# x[[2]]
# })
#
# rm(list = "mona_spec")
#
# info <- pbapply::pblapply(mona_spec, function(x){
# x <- x[[1]]
# x <- x[which(!rownames(x) %in% c("Comments", "Num Peaks")),]
# })
#
# item.list2 <- unique(unlist(pbapply::pblapply(info, function(x){
# rownames(x)
# })))
#
# item.list2 <- item.list2[item.list2 %in% c("Name", "Synon", "InChIKey", "Precursor_type", "Spectrum_type",
# "Instrument_type", "Instrument", "Ion_mode",
# "Collision_energy", "Formula", "ExactMass")]
#
#
#
#
#
# info <- pbapply::pblapply(info, function(x){
# temp <- data.frame("Item" = item.list2, "Value" = NA, stringsAsFactors = FALSE)
# x <- x[rownames(x) %in% temp$Item,, drop = FALSE]
# temp[match(rownames(x), temp[,1]),2] <- x[,1]
# temp <- as.data.frame(t(temp), stringsAsFactors = FALSE)
# temp <- temp[2,,drop = FALSE]
# temp
# })
#
# info <- do.call(rbind, info)
#
# colnames(info) <- item.list2
#
#
# info <- cbind(info, comment5)
#
# rm(list = "comment5")
# save(info, file = "info")
# load("info")
# info2 <- t(apply(info, 1, as.character))
# colnames(info2) <- colnames(info)
#
# rm(list = "info")
#
# info2 <- as.data.frame(info2, stringsAsFactors = FALSE)
#
# ###remove some spectra
# ##Not MS2 spectrum
# spectrum.type <- info2$Spectrum_type
# spectrum.type[is.na(spectrum.type)] <- ""
# remove.idx <- which(info2$Spectrum_type %in% c("MS", "MS1", "MS3", 'MS4'))
# info2 <- info2[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
# ##No polarity
# polarity <- info2[,c("Ion_mode", "ion mode")]
# polarity <- apply(polarity, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# remove.idx <- which(is.na(polarity))
# info2 <- info2[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
#
# ###nature product
# class <- info2$`compound class`
# class[is.na(class)] <- ""
#
# remove.idx <- grep("Natural Product", class, value = FALSE)
# info2 <- info2[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
#
# Compound.name <- info2$Name
# sum(is.na(Compound.name))
#
# Compound.name <- info2$Name
# sum(is.na(Compound.name))
#
# Synonym <- info2$Synon
# sum(is.na(Synonym))
#
# Spectra.adduct <- info2[,c("Precursor_type", "adduct", "ion type")]
#
# Spectra.adduct <- apply(Spectra.adduct, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# Spectra.type <- info2$Spectrum_type
#
# Instrument.type <- info2[,c("Instrument_type", "instrumenttype")]
# Instrument.type <- apply(Instrument.type, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# Instrument <- info2$Instrument
#
# Polarity <- info2[, c("Ion_mode", "ion mode")]
# Polarity <- apply(Polarity, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# Polarity[Polarity == "P"] <- "Positive"
# Polarity[Polarity == "N"] <- "Negative"
#
# CE <- info2[,c("Collision_energy","collision energy voltage")]
#
# CE <- apply(CE, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# CE <- stringr::str_replace_all(string = CE, pattern = "eV|V", replacement = "")
# CE <- stringr::str_trim(CE)
#
#
# Formula <- info2[,c("Formula", "formula")]
#
# Formula <- apply(Formula, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
#
# mz <- info2[,c("ExactMass", "exactmass", "accurate mass")]
# mz <- apply(mz, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# mz <- as.numeric(mz)
#
# SMILES <- info2[,c("SMILES", "smiles")]
# SMILES <- apply(SMILES, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
#
# CAS.ID <- info2[,c("cas", "cas number")]
#
# CAS.ID <- apply(CAS.ID, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
# PubChem.CID <- info2$`pubchem cid`
#
# Chemspider.ID <- info2$chemspider
#
# InChI <- info2$InChI
#
# MoNA.ID <- info2$accession
#
# Submitter <- info2$submitter
#
# KEGG.ID <- info2$kegg
#
# Chebi.ID <- info2$chebi
#
# PubChem.ID <- info2[,c("pubchem", "pubmed id", "PubChem")]
#
# PubChem.ID <- apply(PubChem.ID, 1, function(x){
# x <- as.character(x)
# if(all(is.na(x))) return(NA)
# x <- x[!is.na(x)]
# return(x[1])
# })
#
#
# Lipidmaps.ID <- info2$lipidmaps
#
#
# Compound.class <- info2$`compound class`
#
# Lipidbank.ID <- info2$lipidbank
#
# HMDB.ID <- info2$hmdb
#
# PubChem.SID <- info2$`pubchem sid`
#
#
# InChIKey <- info2$InChIKey
# InChI <- info2$InChI
# Spectra.adduct <- info2$Precursor_type
#
#
# spectra.info <- data.frame(Lab.ID = NA, Compound.name, mz, RT = NA, CAS.ID, HMDB.ID, KEGG.ID, Formula,
# CE, Chebi.ID, Chemspider.ID, Compound.class, InChI, InChIKey, Instrument,
# Instrument.type, Polarity, PubChem.CID, PubChem.ID, PubChem.SID, SMILES,
# Spectra.adduct, Spectra.type, Submitter,
# Synonym,
# stringsAsFactors = FALSE
# )
#
# save(spectra.info, file = "spectra.info")
# save(spectra.data, file = "spectra.data")
# load("spectra.data")
# ##remove some spectrum
# remove.idx <- which(is.na(spectra.info$mz))
#
# spectra.info <- spectra.info[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
# length(spectra.data)
# dim(spectra.info)
#
# remove.idx <- which(is.na(spectra.info$Formula))
#
# spectra.info <- spectra.info[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
# length(spectra.data)
# dim(spectra.info)
#
# remove.idx <- which(is.na(spectra.info$Compound.name))
#
#
# table(spectra.info$Submitter)
#
# remove.idx <- c(grep("(Markus Kohlhoff)|(GNPS Collaboration)|(Arpana Vaniya)", spectra.info$Submitter))
#
# table(spectra.info$Submitter[remove.idx])
#
# spectra.info[grep("Arpana Vaniya", spectra.info$Submitter), "Compound.name"]
#
# spectra.info <- spectra.info[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
# length(spectra.data)
# dim(spectra.info)
#
# ##remove some duplicated spectra
# temp.id <- apply(spectra.info[,c(2, 8, 15, 17, 22, 24, 9)], 1, function(x){
# paste(as.character(x), collapse = ";")
# })
#
# unique.temp.id <- unique(temp.id)
#
# temp.idx <- which(unlist(pbapply::pblapply(unique.temp.id, function(x){
# sum(x == temp.id)
# })) > 1)
#
#
# remove.idx <- which(duplicated(temp.id))
#
# spectra.info <- spectra.info[-remove.idx,]
# spectra.data <- spectra.data[-remove.idx]
#
# length(spectra.data)
# dim(spectra.info)
#
#
# # spectra.info$CE <- stringr::str_repla
#
#
#
# Lab.ID1 <- apply(spectra.info[,c(2, 8, 15, 17, 22, 24, 9)], 1, function(x){
# paste(as.character(x), collapse = ";")
# })
#
# Lab.ID2 <- apply(spectra.info[,c(2, 8, 15, 17, 22, 24)], 1, function(x){
# paste(as.character(x), collapse = ";")
# })
#
#
# spectra.info$Lab.ID <- Lab.ID2
#
# names(spectra.data) <- Lab.ID1
#
#
# spectra.pos <- spectra.data[grep("Positive", Lab.ID1)]
# spectra.neg <- spectra.data[grep("Negative", Lab.ID1)]
#
# unique.lab.id.pos <- unique(grep("Positive", Lab.ID2, value = TRUE))
# unique.lab.id.neg <- unique(grep("Negative", Lab.ID2, value = TRUE))
#
#
# spectra.pos.name2 <- grep("Positive", Lab.ID2, value = TRUE)
# spectra.neg.name2 <- grep("Negative", Lab.ID2, value = TRUE)
#
#
# spectra.pos2 <- pbapply::pblapply(unique.lab.id.pos, function(x){
# temp.idx <- which(x == spectra.pos.name2)
# temp.spectra.pos <- spectra.pos[temp.idx]
# temp.ce <- unlist(lapply(stringr::str_split(string = names(temp.spectra.pos), pattern = ";"), function(x){
# tail(x, 1)
# }))
#
# temp.ce[is.na(temp.ce)] <- paste("Unknown", 1:length(temp.ce[is.na(temp.ce)]), sep = "_")
# names(temp.spectra.pos) <- temp.ce
# temp.spectra.pos
# })
#
#
#
# names(spectra.pos2) <- unique.lab.id.pos
#
#
# spectra.neg2 <- pbapply::pblapply(unique.lab.id.neg, function(x){
# temp.idx <- which(x == spectra.neg.name2)
# temp.spectra.neg <- spectra.neg[temp.idx]
# temp.ce <- unlist(lapply(stringr::str_split(string = names(temp.spectra.neg), pattern = ";"), function(x){
# tail(x, 1)
# }))
#
# temp.ce[is.na(temp.ce)] <- paste("Unknown", 1:length(temp.ce[is.na(temp.ce)]), sep = "_")
# names(temp.spectra.neg) <- temp.ce
# temp.spectra.neg
# })
#
#
#
# names(spectra.neg2) <- unique.lab.id.neg
#
#
# ###change ID
# colnames(spectra.info)
# Lab.ID <- spectra.info$Lab.ID
#
# Lab.ID3 <- apply(spectra.info[,c(2, 8, 15, 22, 24)], 1, function(x){
# paste(as.character(x), collapse = ";")
# })
#
#
# remove.idx <- which(duplicated(Lab.ID3))
#
# Lab.ID <- Lab.ID[-remove.idx]
# Lab.ID3 <- Lab.ID3[-remove.idx]
#
# spectra.info2 <- spectra.info[-remove.idx,]
#
# spectra.info2$Lab.ID <- paste("MONA", 1:nrow(spectra.info2), sep = "_")
#
#
# sum(is.na(match(stringr::str_replace(string = names(spectra.pos2), pattern = "Positive;", replacement = ""),
# Lab.ID3)))
#
#
# names(spectra.pos2) <- spectra.info2$Lab.ID[match(stringr::str_replace(string = names(spectra.pos2), pattern = "Positive;", replacement = ""),
# Lab.ID3)]
#
#
# sum(is.na(match(stringr::str_replace(string = names(spectra.neg2), pattern = "Negative;", replacement = ""),
# Lab.ID3)))
#
#
# names(spectra.neg2) <- spectra.info2$Lab.ID[match(stringr::str_replace(string = names(spectra.neg2), pattern = "Negative;", replacement = ""),
# Lab.ID3)]
#
#
# intersect(names(spectra.pos2), names(spectra.neg2))
#
#
# Spectra <- list("Spectra.positive" = spectra.pos2,
# "Spectra.negative" = spectra.neg2)
#
#
# database.info <- list("Version" = "0.0.1",
# "Source" = "MoNA",
# "Link" = "http://mona.fiehnlab.ucdavis.edu/",
# "Creater" = "Xiaotao Shen",
# "Email" = "shenxt1990@163.com",
# "RT" = FALSE)
#
#
#
# monaDatabase0.0.1 <- new(Class = "databaseClass",
# database.info = database.info,
# spectra.info = spectra.info2,
# spectra.data = Spectra)
#
# save(monaDatabase0.0.1, file = 'monaDatabase0.0.1', compress = "xz")
#
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