R/curation_MS2_library.R
In jaspershen/metIdentify: Metabolite identification based on MS1 and MS2 spectra
# # ###this code is ued for curation for MS2 library
# # ##MoNA
# # all_speatra_list <- readr::read_csv("D:/study/database and library/MoNA/MoNA-export-All_Spectra-identifier-table-ids/MoNA-export-All_Spectra-identifier-table.csv")
# # all_spectra_image <- readr::read_csv("D:/study/database and library/MoNA/MoNA-export-All_Spectra-spectrum-images-png/MoNA-export-All_Spectra-spectrum-images.csv")
# #
# # mona_spec <- readMSP_MoNA(file = "D:/study/database and library/MoNA/MoNA-export-All_Spectra-msp/MoNA-export-All_Spectra.msp")
# # save(mona_spec, file = "mona_spec", compress = "xz")
# #
# # #instrument_type
# #
# # instrument_type <- lapply(mona_spec, function(x){
# # as.character(x[[1]]["Instrument_type", 1])
# # })
# #
# # instrument_type2 <- unlist(instrument_type)
# #
# # instrument_type3 <- instrument_type2[!is.na(instrument_type2)]
# # table(instrument_type3)
# #
# # unique(instrument_type3)
# #
# #
# # ####NIST
# #
# #
# # ####METLIN
# #
# #
# # ####zhulab in-house
# #
# #
# #
# #
# # ####MassBank library
# # setwd("D:/study/database and library/MassBank")
# # file <- dir()
# # massbank <- list()
# #
# # for(i in 1:length(file)){
# # cat(i, " ")
# # load(file[i])
# # massbank <- c(massbank, get(gsub(pattern = ".rdata", replacement = "", x = file[i])))
# # }
# #
# # save(massbank, file = "massbank.rdata")
# #
# # massbank[[1]]
# #
# #
# # instrument <- lapply(massbank, function(x){
# # x[[1]][9, 2]
# # })
# #
# # instrument <- unlist(instrument)
# # table(instrument)
# #
# # polarity <- lapply(massbank, function(x){
# # x[[1]][11, 2]
# # })
# #
# # polarity <- unlist(polarity)
# #
# # table(polarity)
# #
# # ce <- lapply(massbank, function(x){
# # x[[1]][12, 2]
# # })
# #
# # ce <- unlist(ce)
# # table(ce)
# #
# #
# #
# #
# #
# #
# # names(zhuMetlib)
# #
# # zhuMetlib.compound <- zhuMetlib[[1]]
# # zhuMetlib.compound.pos <- zhuMetlib.compound[[1]]
# # zhuMetlib.compound.neg <- zhuMetlib.compound[[2]]
# #
# # zhuMetlib.meta <- zhuMetlib[[2]]
# # zhuMetlib.meta.compound <- zhuMetlib.meta[[1]]
# # zhuMetlib.meta.pos <- zhuMetlib.meta[[2]]
# # zhuMetlib.meta.neg <- zhuMetlib.meta[[3]]
# #
# #
# #
# #
# # instrument <- lapply(massbank, function(x){
# # x[[1]][9, 2]
# # })
# #
# # instrument <- unlist(instrument)
# #
# # ##only LC-ESI-QTOF, MALDI-TOFTOF, GC-EI-TOF, LC-ESI-ITTOF, ESI-ITTOF,APCI-ITTOF,LC-ESI-TOF
# # #MALDI-TOF, CE-ESI-TOF, ESI-QTOF are remained
# #
# # idx <- which(instrument %in% c("LC-ESI-QTOF",
# # "MALDI-TOFTOF", "GC-EI-TOF",
# # "LC-ESI-ITTOF", "ESI-ITTOF",
# # "APCI-ITTOF", "LC-ESI-TOF",
# # "MALDI-TOF", "CE-ESI-TOF", "ESI-QTOF"
# # ))
# #
# # massbank1 <- massbank[idx]
# #
# #
# #
# # polarity <- lapply(massbank1, function(x){
# # x[[1]][11, 2]
# # })
# #
# # polarity <- unlist(polarity)
# # massbank.pos <- massbank1[which(polarity == "POSITIVE")]
# # massbank.neg <- massbank1[which(polarity == "NEGATIVE")]
# #
# #
# # ce <- lapply(massbank1, function(x){
# # x[[1]][12, 2]
# # })
# #
# # ce <- unlist(ce)
# # table(ce)
# #
# # colnames(zhuMetlib.meta.compound)
# #
# # name <- unlist(lapply(massbank1, function(x){
# # x[[1]][1,2]
# # }))
# #
# # name <- unlist(lapply(strsplit(name, split = ';'), function(x) x[1]))
# #
# # formula <- unlist(lapply(massbank1, function(x){
# # x[[1]][2,2]
# # }))
# #
# # cas <- unlist(lapply(massbank1, function(x){
# # x[[1]][6,2]
# # }))
# #
# # pubchem <- unlist(lapply(massbank1, function(x){
# # x[[1]][7,2]
# # }))
# #
# # mz <- unlist(lapply(massbank1, function(x){
# # x[[1]][3,2]
# # }))
# #
# # mz <- as.numeric(mz)
# #
# # labid <- paste("MB", 1:length(massbank1), sep = "")
# #
# # hmdb <- rep(NA, length(mz))
# #
# # colnames(zhuMetlib.meta.compound)
# # meta.compound <- data.frame(labid, name, mz, formula, cas, hmdb, stringsAsFactors = FALSE)
# #
# # meta.pos <- data.frame(labid, mz, "10ppm", "qc1", stringsAsFactors = FALSE)[which(polarity == "POSITIVE"),]
# # colnames(meta.pos)[3:4] <- c("ppm", "qc")
# # meta.pos <- list(meta.pos)
# # names(meta.pos) <- "30"
# #
# # meta.neg <- data.frame(labid, mz, "10ppm", "qc1", stringsAsFactors = FALSE)[which(polarity == "NEGATIVE"),]
# # colnames(meta.neg)[3:4] <- c("ppm", "qc")
# # meta.neg <- list(meta.neg)
# # names(meta.neg) <- "30"
# #
# #
# #
# #
# # compound.pos <- lapply(massbank.pos, function(x) x[[2]])
# # compound.pos <- lapply(compound.pos, function(x){
# # colnames(x)[2] <- "intensity"
# # x <- list(x)
# # names(x) <- "30"
# # x
# # })
# #
# # names(compound.pos) <- labid[which(polarity == "POSITIVE")]
# #
# # names(zhuMetlib)
# #
# # compound.neg <- lapply(massbank.neg, function(x) x[[2]])
# # compound.neg <- lapply(compound.neg, function(x){
# # colnames(x)[2] <- "intensity"
# # x <- list(x)
# # names(x) <- "30"
# # x
# # })
# #
# # names(compound.neg) <- labid[which(polarity == "NEGATIVE")]
# # #
# # # zhuMetlib.compound <- zhuMetlib[[1]]
# # # zhuMetlib.compound.pos <- zhuMetlib.compound[[1]]
# # # zhuMetlib.compound.neg <- zhuMetlib.compound[[2]]
# # #
# # # zhuMetlib.meta <- zhuMetlib[[2]]
# # # zhuMetlib.meta.compound <- zhuMetlib.meta[[1]]
# # # zhuMetlib.meta.pos <- zhuMetlib.meta[[2]]
# # # zhuMetlib.meta.neg <- zhuMetlib.meta[[3]]
# #
# # compound <- list(compound.pos, compound.neg)
# # names(compound) <- c("pos", "neg")
# #
# # meta <- list(meta.compound, meta.pos, meta.neg)
# # names(meta) <- names(zhuMetlib.meta)
# #
# # massBankLib <- list(compound, meta)
# # names(massBankLib) <- names(zhuMetlib)
# #
# #
# # save(massBankLib, file = "massBankLib")
# #
# #
# # names(massBankLib)
# # names(zhuMetlib)
# #
# #
# # names(massBankLib[[1]])
# # names(zhuMetlib[[1]])
# #
# #
# # names(massBankLib[[1]][[1]])
# # names(zhuMetlib[[1]][[1]])
# #
# # names(massBankLib[[2]])
# # names(zhuMetlib[[2]])
# #
# # names(massBankLib[[2]][[1]])
# # names(zhuMetlib[[2]][[1]])
# #
# #
# # names(massBankLib[[2]][[2]])
# # names(zhuMetlib[[2]][[2]])
# #
# #
# # load("mz")
# #
# # cbind(massBankLib$meta$compound$mz, mz)
# #
# # temp.idx <- match(massBankLib$meta$compound$name[which(is.na(mz))],
# # unlist(lapply(massbank, function(x) strsplit(x$ms2.info[1,2], split = ";")[[1]][1])))
# #
# #
# #
# # mz[which(is.na(mz))] <-
# # as.numeric(unlist(lapply(massbank[temp.idx], function(x) x$ms2.info[3,2])))
# #
# #
# #
# # temp.idx.pos <- match(massBankLib$meta$pos$`30`$labid, massBankLib$meta$compound$labid)
# # temp.idx.neg <- match(massBankLib$meta$neg$`30`$labid, massBankLib$meta$compound$labid)
# #
# #
# # massBankLib$meta$pos$`30`$mz <- massBankLib$meta$compound$mz[temp.idx.pos]
# #
# # massBankLib$meta$neg$`30`$mz <- massBankLib$meta$compound$mz[temp.idx.neg]
# #
# # massBankLib$meta$compound$mz <- mz
# # save(massBankLib, file = "massBankLib")
# #
# #
# #
# #
# #
# #
# #
# #
#
# ###Massbank data
# setwd("D:/my github/metTools/data")
# load("massbank.rdata")
# instrument <- lapply(massbank, function(x){
# x[[1]][9, 2]
# })
#
# instrument <- unlist(instrument)
# table(instrument)
#
# ce <- unlist(lapply(massbank, function(x){
# x[[1]][12, 2]
# }))
#
# ##polarity
# polarity <- unlist(lapply(massbank, function(x){
# x[[1]][11, 2]
# }))
#
# table(polarity)
#
# massbank.pos <- massbank[which(polarity == "POSITIVE")]
# massbank.neg <- massbank[which(polarity == "NEGATIVE")]
#
# ##creat met.compound information
# names(zhuMetlib)
# zhuMetlib.compound <- zhuMetlib[[1]]
# zhuMetlib.compound.pos <- zhuMetlib.compound[[1]]
# zhuMetlib.compound.neg <- zhuMetlib.compound[[2]]
#
# zhuMetlib.meta <- zhuMetlib[[2]]
# zhuMetlib.meta.compound <- zhuMetlib.meta[[1]]
# zhuMetlib.meta.pos <- zhuMetlib.meta[[2]]
# zhuMetlib.meta.neg <- zhuMetlib.meta[[3]]
#
# colnames(zhuMetlib.meta.compound)
#
# name <- unlist(lapply(massbank, function(x){
# x[[1]][1,2]
# }))
#
# name <- unlist(lapply(strsplit(name, split = ';'), function(x) x[1]))
#
# formula <- unlist(lapply(massbank, function(x){
# x[[1]][2,2]
# }))
#
# cas <- unlist(lapply(massbank, function(x){
# x[[1]][6,2]
# }))
#
# pubchem <- unlist(lapply(massbank, function(x){
# x[[1]][7,2]
# }))
#
# mz <- unlist(lapply(massbank, function(x){
# x[[1]][3,2]
# }))
#
# mz <- as.numeric(mz)
#
# labid <- paste("MB", 1:length(massbank), sep = "")
#
# hmdb <- rep(NA, length(mz))
#
# massbank[[1]]$ms2.info$name
#
# colnames(zhuMetlib.meta.compound)
# smile <- unlist(lapply(massbank, function(x){
# x[[1]][4,2]
# }))
#
# iupac <- unlist(lapply(massbank, function(x){
# x[[1]][5,2]
# }))
#
# pubchem <- unlist(lapply(massbank, function(x){
# x[[1]][7,2]
# }))
#
#
# chemspider <- unlist(lapply(massbank, function(x){
# x[[1]][8,2]
# }))
#
# instrument.type <- unlist(lapply(massbank, function(x){
# x[[1]][9,2]
# }))
#
#
# instrument <- unlist(lapply(massbank, function(x){
# x[[1]][10,2]
# }))
#
#
# ce <- unlist(lapply(massbank, function(x){
# x[[1]][12,2]
# }))
#
#
# adduct <- unlist(lapply(massbank, function(x){
# x[[1]][14,2]
# }))
#
# precursor.mz <- adduct <- unlist(lapply(massbank, function(x){
# x[[1]][13,2]
# }))
#
#
# meta.compound <- data.frame(labid, name, mz, formula, cas, hmdb,
# smile, iupac, pubchem, chemspider,
# instrument.type, instrument, ce,
# adduct, precursor.mz,
# stringsAsFactors = FALSE)
#
# meta.pos <- data.frame(labid, mz, "10ppm", "qc1",
# stringsAsFactors = FALSE)[which(polarity == "POSITIVE"),]
# colnames(meta.pos)[3:4] <- c("ppm", "qc")
# meta.pos <- list(meta.pos)
# names(meta.pos) <- "30"
#
# meta.neg <- data.frame(labid, mz, "10ppm", "qc1", stringsAsFactors = FALSE)[which(polarity == "NEGATIVE"),]
# colnames(meta.neg)[3:4] <- c("ppm", "qc")
# meta.neg <- list(meta.neg)
# names(meta.neg) <- "30"
#
# compound.pos <- lapply(massbank.pos, function(x) x[[2]])
# compound.pos <- lapply(compound.pos, function(x){
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.pos) <- labid[which(polarity == "POSITIVE")]
#
# compound.neg <- lapply(massbank.neg, function(x) x[[2]])
# compound.neg <- lapply(compound.neg, function(x){
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.neg) <- labid[which(polarity == "NEGATIVE")]
#
#
# compound <- list(compound.pos, compound.neg)
# names(compound) <- c("pos", "neg")
#
# meta <- list(meta.compound, meta.pos, meta.neg)
# names(meta) <- names(zhuMetlib.meta)
#
# massBankLib <- list(compound, meta)
# names(massBankLib) <- names(zhuMetlib)
#
#
# save(massBankLib, file = "massBankLib.rda", compress = "xz")
#
#
# ####MoNA
# setwd("D:/study/database and library/MoNA/")
# mona_spec <- readMSP_MoNA(file = "D:/study/database and library/MoNA/MoNA-export-All_Spectra-msp/MoNA-export-All_Spectra.msp")
#
# save(mona_spec, file = "mona_spec", compress = "xz")
# # load("mona_spec")
# ##polarity
# polarity <- unlist(lapply(mona_spec, function(x){
# as.character(x[[1]]["Ion_mode", 1])
# }))
#
# table(polarity)
# ###peak with no polarity are removed
# mona_spec <- mona_spec[which(!is.na(polarity))]
# mona.pos <- mona_spec[which(polarity == "P")]
# mona.neg <- mona_spec[which(polarity == "N")]
#
# ##creat met.compound information
# names(zhuMetlib)
# zhuMetlib.compound <- zhuMetlib[[1]]
# zhuMetlib.compound.pos <- zhuMetlib.compound[[1]]
# zhuMetlib.compound.neg <- zhuMetlib.compound[[2]]
#
# zhuMetlib.meta <- zhuMetlib[[2]]
# zhuMetlib.meta.compound <- zhuMetlib.meta[[1]]
# zhuMetlib.meta.pos <- zhuMetlib.meta[[2]]
# zhuMetlib.meta.neg <- zhuMetlib.meta[[3]]
#
# colnames(zhuMetlib.meta.compound)
#
# name <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Name",1]
# }))
# sum(is.na(name))
# temp.idx1 <- which(!is.na(name))
# # name <- unlist(lapply(strsplit(name, split = ';'), function(x) x[1]))
#
# formula <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Formula",1]
# }))
#
# sum(is.na(formula))
# temp.idx2 <- which(!is.na(formula))
#
#
#
# cas <- rep(NA, length(mona_spec))
#
# pubchem <- rep(NA, length(mona_spec))
#
# mz <- unlist(lapply(mona_spec, function(x){
# x[[1]]["ExactMass",1]
# }))
#
# mz <- as.numeric(mz)
# temp.idx3 <- which(!is.na(mz))
#
# hmdb <- rep(NA, length(mona_spec))
#
# temp.idx <- intersect(intersect(temp.idx1, temp.idx2), temp.idx3)
#
# mona_spec <- mona_spec[temp.idx]
# labid <- paste("MONA", 1:length(mona_spec), sep = "")
#
# ##polarity
# polarity <- unlist(lapply(mona_spec, function(x){
# as.character(x[[1]]["Ion_mode", 1])
# }))
#
# table(polarity)
#
# mona.pos <- mona_spec[which(polarity == "P")]
# mona.neg <- mona_spec[which(polarity == "N")]
#
#
# name <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Name",1]
# }))
# sum(is.na(name))
#
# formula <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Formula",1]
# }))
#
# sum(is.na(formula))
#
# cas <- rep(NA, length(mona_spec))
#
# smile <- rep(NA, length(mona_spec))
#
# pubchem <- rep(NA, length(mona_spec))
#
# mz <- unlist(lapply(mona_spec, function(x){
# x[[1]]["ExactMass",1]
# }))
#
# mz <- as.numeric(mz)
#
# hmdb <- rep(NA, length(mona_spec))
#
# rownames(mona_spec[[1]]$info)
#
# colnames(zhuMetlib.meta.compound)
#
# InChIKey <- unlist(lapply(mona_spec, function(x){
# as.character(x[[1]]["InChIKey",1])
# }))
#
#
# instrument.type <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Instrument_type",1]
# }))
#
#
# instrument <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Instrument",1]
# }))
#
#
# ce <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Collision_energy",1]
# }))
#
#
# adduct <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Precursor_type",1]
# }))
#
#
# comment <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Comments",1]
# }))
#
# precursor.mz <- unlist(lapply(mona_spec, function(x){
# x[[1]]["PrecursorMZ",1]
# }))
#
#
# meta.compound <- data.frame(labid, name, mz, formula, cas, hmdb,
# smile, adduct,
# instrument.type, instrument, ce,
# adduct, precursor.mz, comment,
# stringsAsFactors = FALSE)
#
# meta.pos <- data.frame(labid, mz, "10ppm", "qc1",
# stringsAsFactors = FALSE)[which(polarity == "P"),]
# colnames(meta.pos)[3:4] <- c("ppm", "qc")
# meta.pos <- list(meta.pos)
# names(meta.pos) <- "30"
#
# meta.neg <- data.frame(labid, mz, "10ppm", "qc1",
# stringsAsFactors = FALSE)[which(polarity == "N"),]
# colnames(meta.neg)[3:4] <- c("ppm", "qc")
# meta.neg <- list(meta.neg)
# names(meta.neg) <- "30"
#
# compound.pos <- lapply(mona.pos, function(x) x[[2]])
# compound.pos <- lapply(compound.pos, function(x){
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.pos) <- labid[which(polarity == "P")]
#
# compound.neg <- lapply(mona.neg, function(x) x[[2]])
# compound.neg <- lapply(compound.neg, function(x){
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.neg) <- labid[which(polarity == "N")]
#
#
# compound <- list(compound.pos, compound.neg)
# names(compound) <- c("pos", "neg")
#
# meta <- list(meta.compound, meta.pos, meta.neg)
# names(meta) <- names(zhuMetlib.meta)
#
# monaLib <- list(compound, meta)
# names(monaLib) <- names(zhuMetlib)
#
#
# save(monaLib, file = "monaLib.rda", compress = "xz")
#
#
#
#
# ###metlin
# setwd("D:/study/database and library/metlin")
# load("metlinlib.rdata")
# names(metlinlib)
# metlinLib <- metlinlib[[1]]
# names(metlinLib)
#
# head(metlinLib$meta$compound)
#
# temp.pos <- mapply(function(x,y){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# },
# x = metlinLib$compound$pos,
# y = names(metlinLib$compound$pos))
#
# temp.pos <- do.call(what = c, args = temp.pos)
#
# names(temp.pos) <- unlist(lapply(stringr::str_split(string = names(temp.pos), pattern = "\\."), function(x){
# x[2]
# }))
#
#
#
#
# temp.neg <- mapply(function(x,y){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# },
# x = metlinLib$compound$neg,
# y = names(metlinLib$compound$neg))
#
# temp.neg <- do.call(what = c, args = temp.neg)
#
# names(temp.neg) <- unlist(lapply(stringr::str_split(string = names(temp.neg), pattern = "\\."), function(x){
# x[2]
# }))
#
#
# temp.name <- unique(c(names(temp.pos), names(temp.neg)))
#
#
# temp.compound <- metlinLib$meta$compound
#
# temp.compound <- apply(temp.compound, 1, function(x){
# x <- t(data.frame(x))
# x <- as.data.frame(x)
# new.id <- grep(pattern = x[1,1], x = temp.name, value = TRUE)
# x <- x[rep(1, length(new.id)),]
# x$labid <- new.id
# rownames(x) <- NULL
# x
# })
#
# temp.compound <- do.call(rbind, temp.compound)
#
# rownames(temp.compound) <- NULL
#
# names(metlinLib$meta$pos)
#
#
# temp.meta.pos <- metlinLib$meta$pos
# temp.meta.neg <- metlinLib$meta$neg
#
# temp.meta.pos <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.pos,
# y = names(temp.meta.pos))
#
# temp.meta.neg <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.neg,
# y = names(temp.meta.neg))
#
#
# temp.meta.pos <- do.call(rbind, args = temp.meta.pos)
# temp.meta.neg <- do.call(rbind, args = temp.meta.neg)
#
# rownames(temp.meta.pos) <- NULL
# rownames(temp.meta.neg) <- NULL
#
#
# length(temp.pos)
# dim(temp.meta.pos)
#
# length(temp.neg)
# dim(temp.meta.neg)
#
# temp.pos <- lapply(temp.pos, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.neg <- lapply(temp.neg, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.meta.pos <- list(temp.meta.pos)
# names(temp.meta.pos) <- "30"
#
# temp.meta.neg <- list(temp.meta.neg)
# names(temp.meta.neg) <- "30"
#
# metlinLib$compound$pos <- temp.pos
# metlinLib$compound$neg <- temp.neg
#
# metlinLib$meta$compound <- temp.compound
# metlinLib$meta$pos <- temp.meta.pos
# metlinLib$meta$neg <- temp.meta.neg
#
# save(metlinLib, file = "metlibLib.rda", compress = "xz")
#
#
# ##zhu_nist
# setwd("D:/study/database and library/zhu_nist")
# load("zhuMetlib.rda")
# names(zhuMetlib)
# nistLib <- zhuMetlib
# names(nistLib)
#
# head(nistLib$meta$compound)
#
#
#
# temp.pos <- mapply(function(x,y){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# },
# x = nistLib$compound$pos,
# y = names(nistLib$compound$pos))
#
# temp.pos <- do.call(what = c, args = temp.pos)
#
# names(temp.pos) <- unlist(lapply(stringr::str_split(string = names(temp.pos), pattern = "\\."), function(x){
# x[2]
# }))
#
#
# # for(i in 1:length(nistLib$compound$neg)){
# # cat(i, " ")
# # x <- nistLib$compound$neg[[i]]
# # y <- names(nistLib$compound$neg)[i]
# # if(length(x) != 0){
# # names(x) <- stringr::str_c(y, names(x), sep = "_")
# # }
# #
# # }
#
# temp.neg <- mapply(function(x,y){
# if(length(x) != 0){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# }
# },
# x = nistLib$compound$neg,
# y = names(nistLib$compound$neg))
#
# temp.neg <- do.call(what = c, args = temp.neg)
#
# names(temp.neg) <- unlist(lapply(stringr::str_split(string = names(temp.neg), pattern = "\\."), function(x){
# x[2]
# }))
#
#
# temp.name <- unique(c(names(temp.pos), names(temp.neg)))
#
#
# temp.compound <- nistLib$meta$compound
#
# temp.compound <- apply(temp.compound, 1, function(x){
# x <- t(data.frame(x))
# x <- as.data.frame(x)
# new.id <- grep(pattern = x[1,1], x = temp.name, value = TRUE)
# x <- x[rep(1, length(new.id)),]
# x$labid <- new.id
# rownames(x) <- NULL
# x
# })
#
# temp.compound <- do.call(rbind, temp.compound)
#
# rownames(temp.compound) <- NULL
#
# names(nistLib$meta$pos)
#
#
# temp.meta.pos <- nistLib$meta$pos
# temp.meta.neg <- nistLib$meta$neg
#
# temp.meta.pos <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.pos,
# y = names(temp.meta.pos))
#
# temp.meta.neg <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.neg,
# y = names(temp.meta.neg))
#
#
# temp.meta.pos <- do.call(rbind, args = temp.meta.pos)
# temp.meta.neg <- do.call(rbind, args = temp.meta.neg)
#
# rownames(temp.meta.pos) <- NULL
# rownames(temp.meta.neg) <- NULL
#
#
# length(temp.pos)
# dim(temp.meta.pos)
#
# length(temp.neg)
# dim(temp.meta.neg)
#
# temp.pos <- lapply(temp.pos, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.neg <- lapply(temp.neg, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.meta.pos <- list(temp.meta.pos)
# names(temp.meta.pos) <- "30"
#
# temp.meta.neg <- list(temp.meta.neg)
# names(temp.meta.neg) <- "30"
#
# nistLib$compound$pos <- temp.pos
# nistLib$compound$neg <- temp.neg
#
# nistLib$meta$compound <- temp.compound
# nistLib$meta$pos <- temp.meta.pos
# nistLib$meta$neg <- temp.meta.neg
#
# save(nistLib, file = "nistLib.rda", compress = "xz")
#
#
#
# ###orbitrap
# setwd("D:/study/database and library/nist_orbitrap")
# load("orbitrapMetlib.rda")
# names(orbitrapMetlib)
# orbitrapLib <- orbitrapMetlib
# names(orbitrapLib)
#
# head(orbitrapLib$meta$compound)
#
#
#
# temp.pos <- mapply(function(x,y){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# },
# x = orbitrapLib$compound$pos,
# y = names(orbitrapLib$compound$pos))
#
# temp.pos <- do.call(what = c, args = temp.pos)
#
# names(temp.pos) <- unlist(lapply(stringr::str_split(string = names(temp.pos), pattern = "\\."), function(x){
# x[2]
# }))
#
#
# # for(i in 1:length(orbitrapLib$compound$neg)){
# # cat(i, " ")
# # x <- orbitrapLib$compound$neg[[i]]
# # y <- names(orbitrapLib$compound$neg)[i]
# # if(length(x) != 0){
# # names(x) <- stringr::str_c(y, names(x), sep = "_")
# # }
# #
# # }
#
# temp.neg <- mapply(function(x,y){
# if(length(x) != 0){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# }
# },
# x = orbitrapLib$compound$neg,
# y = names(orbitrapLib$compound$neg))
#
# temp.neg <- do.call(what = c, args = temp.neg)
#
# names(temp.neg) <- unlist(lapply(stringr::str_split(string = names(temp.neg), pattern = "\\."), function(x){
# x[2]
# }))
#
#
# temp.name <- unique(c(names(temp.pos), names(temp.neg)))
#
#
# temp.compound <- orbitrapLib$meta$compound
#
# temp.compound <- apply(temp.compound, 1, function(x){
# x <- t(data.frame(x))
# x <- as.data.frame(x)
# new.id <- grep(pattern = x[1,1], x = temp.name, value = TRUE)
# x <- x[rep(1, length(new.id)),]
# x$labid <- new.id
# rownames(x) <- NULL
# x
# })
#
# temp.compound <- do.call(rbind, temp.compound)
#
# rownames(temp.compound) <- NULL
#
# names(orbitrapLib$meta$pos)
#
#
# temp.meta.pos <- orbitrapLib$meta$pos
# temp.meta.neg <- orbitrapLib$meta$neg
#
# temp.meta.pos <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.pos,
# y = names(temp.meta.pos))
#
# temp.meta.neg <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.neg,
# y = names(temp.meta.neg))
#
#
# temp.meta.pos <- do.call(rbind, args = temp.meta.pos)
# temp.meta.neg <- do.call(rbind, args = temp.meta.neg)
#
# rownames(temp.meta.pos) <- NULL
# rownames(temp.meta.neg) <- NULL
#
#
# length(temp.pos)
# dim(temp.meta.pos)
#
# length(temp.neg)
# dim(temp.meta.neg)
#
# temp.pos <- lapply(temp.pos, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.neg <- lapply(temp.neg, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.meta.pos <- list(temp.meta.pos)
# names(temp.meta.pos) <- "30"
#
# temp.meta.neg <- list(temp.meta.neg)
# names(temp.meta.neg) <- "30"
#
# orbitrapLib$compound$pos <- temp.pos
# orbitrapLib$compound$neg <- temp.neg
#
# orbitrapLib$meta$compound <- temp.compound
# orbitrapLib$meta$pos <- temp.meta.pos
# orbitrapLib$meta$neg <- temp.meta.neg
#
# save(orbitrapLib, file = "orbitrapLib.rda", compress = "xz")
#
#
# ###HMDB
# setwd("D:/study/database and library/HMDB/hmdb_experimental_msms_spectra")
# library(XML)
# library("methods")
#
# file <- dir()
# hmdbLib <- vector(mode = "list", length = length(file))
# for(i in 1:length(file)){
# cat(i, " ")
# temp.file <- file[i]
# result <- xmlParse(file = temp.file)
# rootnode <- xmlRoot(result)
# info <- xmlSApply(rootnode, function(x) xmlSApply(x, xmlValue))
# names(info) <- unname(names(rootnode))
# info <- lapply(info, unname)
# ms2.mz <- sapply(getNodeSet(doc = rootnode[[26]], path = "//mass-charge"), xmlValue)
# ms2.int <- sapply(getNodeSet(doc = rootnode[[26]], path = "//intensity"), xmlValue)
# ms2 <- data.frame("mz" = ms2.mz, "intensity" = ms2.int,
# stringsAsFactors = FALSE)
# info[[26]] <- ms2
#
# ms2.info <- info[c(10, 17, 18, 24, 25)]
# ms2.info <- lapply(ms2.info, function(x){
# if(length(x) == 0){
# x <- NA
# }
# x
# })
# ms2.spec <- info[[26]]
#
# ms2.info <- do.call(rbind, ms2.info)
# ms2.info <- data.frame("name" = rownames(ms2.info), "value" = ms2.info[,1],
# stringsAsFactors = FALSE)
# ms2.info <- tibble::as_tibble(ms2.info)
#
# temp.spec <- list(ms2.info = ms2.info, ms2.spec = ms2.spec)
# hmdbLib[[i]] <- temp.spec
#
# }
#
# hmdb <- hmdbLib
# save(hmdb, file = "hmdb")
# load("hmdb")
# ##polarity
# polarity <- unlist(lapply(hmdb, function(x){
# x[[1]][3, 2]
# }))
#
# temp.idx1 <- which(polarity != "N/A")
#
# table(polarity)
#
# hmdb <- hmdb[temp.idx1]
#
# polarity <- unlist(lapply(hmdb, function(x){
# x[[1]][3, 2]
# }))
#
# polarity <- stringr::str_to_lower(polarity)
#
# instrument <- lapply(hmdb, function(x){
# x[[1]][1, 2]
# })
#
# instrument <- unlist(instrument)
# table(instrument)
#
# ce <- unlist(lapply(hmdb, function(x){
# x[[1]][2, 2]
# }))
#
# sum(is.na(ce))
#
#
#
# ##creat met.compound information
# names(zhuMetlib)
# zhuMetlib.compound <- zhuMetlib[[1]]
# zhuMetlib.compound.pos <- zhuMetlib.compound[[1]]
# zhuMetlib.compound.neg <- zhuMetlib.compound[[2]]
#
# zhuMetlib.meta <- zhuMetlib[[2]]
# zhuMetlib.meta.compound <- zhuMetlib.meta[[1]]
# zhuMetlib.meta.pos <- zhuMetlib.meta[[2]]
# zhuMetlib.meta.neg <- zhuMetlib.meta[[3]]
#
# colnames(zhuMetlib.meta.compound)
#
# hmdb.id <- unlist(lapply(hmdb, function(x){
# x[[1]][4,2]
# }))
#
# hmdb.id <- unname(hmdb.id)
# hmdb.id <- stringr::str_replace(string = hmdb.id, pattern = "00", replacement = "")
#
#
# load("G:/Project/MetDNA/annotation and identification/annotation/HMDB compound database/hmdbAllinf.rda")
#
# name <- as.character(hmdbAllinf$Name[match(hmdb.id, hmdbAllinf$HMDBID)])
# sum(is.na(name))
#
#
# formula <- as.character(hmdbAllinf$Formula[match(hmdb.id, hmdbAllinf$HMDBID)])
#
# cas <- as.character(hmdbAllinf$CAS_Registry_Number[match(hmdb.id, hmdbAllinf$HMDBID)])
#
# pubchem <- rep(NA, length(name))
# cas <- as.character(hmdbAllinf$CAS_Registry_Number[match(hmdb.id, hmdbAllinf$HMDBID)])
#
#
# mz <- as.character(hmdbAllinf$MonoisotopicMass[match(hmdb.id, hmdbAllinf$HMDBID)])
#
# mz <- as.numeric(mz)
#
# labid <- paste("HM", 1:length(hmdb), sep = "")
#
# # hmdb.id <- rep(NA, length(mz))
#
# hmdb[[1]]$ms2.info$name
#
# colnames(zhuMetlib.meta.compound)
#
# metlinid <- as.character(hmdbAllinf$MetlinID[match(hmdb.id, hmdbAllinf$HMDBID)])
#
#
# keggid <- as.character(hmdbAllinf$KEGGID[match(hmdb.id, hmdbAllinf$HMDBID)])
#
# smpdbid <- as.character(hmdbAllinf$SMPDB_ID[match(hmdb.id, hmdbAllinf$HMDBID)])
# smile <- as.character(hmdbAllinf$Smiles[match(hmdb.id, hmdbAllinf$HMDBID)])
#
# InChiKey <- as.character(hmdbAllinf$InChiKey[match(hmdb.id, hmdbAllinf$HMDBID)])
# ChemSpider_ID <- as.character(hmdbAllinf$ChemSpider_ID[match(hmdb.id, hmdbAllinf$HMDBID)])
#
#
# meta.compound <- data.frame(labid, name, mz, formula, cas, hmdb.id,
# smile, ChemSpider_ID, metlinid, keggid, smpdbid,
# instrument, ce,InChiKey,
# stringsAsFactors = FALSE)
# meta.compound <- meta.compound[which(!is.na(name) & !is.na(mz) & !is.na(formula)),]
#
# polarity <- polarity[which(!is.na(name) & !is.na(mz) & !is.na(formula))]
#
# hmdb.pos <- hmdb[which(polarity == "positive")]
# hmdb.neg <- hmdb[which(polarity == "negative")]
#
# meta.pos <- data.frame(
# "labid" = meta.compound$labid,
# "mz" = meta.compound$mz,
# "10ppm", "qc1",
# stringsAsFactors = FALSE)[which(polarity == "positive"),]
# colnames(meta.pos)[3:4] <- c("ppm", "qc")
# meta.pos <- list(meta.pos)
# names(meta.pos) <- "30"
#
# meta.neg <- data.frame(
# "labid" = meta.compound$labid,
# "mz" = meta.compound$mz,
# "10ppm", "qc1",
# stringsAsFactors = FALSE)[which(polarity == "negative"),]
#
# colnames(meta.neg)[3:4] <- c("ppm", "qc")
# meta.neg <- list(meta.neg)
# names(meta.neg) <- "30"
#
# compound.pos <- lapply(hmdb.pos, function(x) x[[2]])
#
#
#
# compound.pos <- lapply(compound.pos, function(x){
# if(nrow(x) == 0) return(NA)
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.pos) <- labid[which(polarity == "positive")]
#
# temp.idx.pos <- which(!unlist(lapply(compound.pos, is.na)))
# compound.pos <- compound.pos[temp.idx.pos]
#
# compound.neg <- lapply(hmdb.neg, function(x) x[[2]])
# compound.neg <- lapply(compound.neg, function(x){
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.neg) <- labid[which(polarity == "negative")]
#
#
# compound <- list(compound.pos, compound.neg)
# names(compound) <- c("pos", "neg")
#
# meta <- list(meta.compound, meta.pos, meta.neg)
# names(meta) <- names(zhuMetlib.meta)
#
# hmdbLib <- list(compound, meta)
# names(hmdbLib) <- names(zhuMetlib)
#
#
# save(hmdbLib, file = "hmdbLib.rda", compress = "xz")
#
#
#
#
# library(magrittr)
#
# names(hmdbDatabase0.0.1@spectra.data$Spectra.positive) %in% hmdbDatabase0.0.1@spectra.info$Lab.ID %>%
# which(.) %>%
# `[` (hmdbDatabase0.0.1@spectra.info$HMDB.ID, .) %>%
# unique(.) %>%
# length
#
#
# names(hmdbDatabase0.0.1@spectra.data$Spectra.negative) %in% hmdbDatabase0.0.1@spectra.info$Lab.ID %>%
# which(.) %>%
# `[` (hmdbDatabase0.0.1@spectra.info$HMDB.ID, .) %>%
# unique(.) %>%
# length
jaspershen/metIdentify documentation built on July 26, 2019, 8:54 a.m.
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# # ###this code is ued for curation for MS2 library
# # ##MoNA
# # all_speatra_list <- readr::read_csv("D:/study/database and library/MoNA/MoNA-export-All_Spectra-identifier-table-ids/MoNA-export-All_Spectra-identifier-table.csv")
# # all_spectra_image <- readr::read_csv("D:/study/database and library/MoNA/MoNA-export-All_Spectra-spectrum-images-png/MoNA-export-All_Spectra-spectrum-images.csv")
# #
# # mona_spec <- readMSP_MoNA(file = "D:/study/database and library/MoNA/MoNA-export-All_Spectra-msp/MoNA-export-All_Spectra.msp")
# # save(mona_spec, file = "mona_spec", compress = "xz")
# #
# # #instrument_type
# #
# # instrument_type <- lapply(mona_spec, function(x){
# # as.character(x[[1]]["Instrument_type", 1])
# # })
# #
# # instrument_type2 <- unlist(instrument_type)
# #
# # instrument_type3 <- instrument_type2[!is.na(instrument_type2)]
# # table(instrument_type3)
# #
# # unique(instrument_type3)
# #
# #
# # ####NIST
# #
# #
# # ####METLIN
# #
# #
# # ####zhulab in-house
# #
# #
# #
# #
# # ####MassBank library
# # setwd("D:/study/database and library/MassBank")
# # file <- dir()
# # massbank <- list()
# #
# # for(i in 1:length(file)){
# # cat(i, " ")
# # load(file[i])
# # massbank <- c(massbank, get(gsub(pattern = ".rdata", replacement = "", x = file[i])))
# # }
# #
# # save(massbank, file = "massbank.rdata")
# #
# # massbank[[1]]
# #
# #
# # instrument <- lapply(massbank, function(x){
# # x[[1]][9, 2]
# # })
# #
# # instrument <- unlist(instrument)
# # table(instrument)
# #
# # polarity <- lapply(massbank, function(x){
# # x[[1]][11, 2]
# # })
# #
# # polarity <- unlist(polarity)
# #
# # table(polarity)
# #
# # ce <- lapply(massbank, function(x){
# # x[[1]][12, 2]
# # })
# #
# # ce <- unlist(ce)
# # table(ce)
# #
# #
# #
# #
# #
# #
# # names(zhuMetlib)
# #
# # zhuMetlib.compound <- zhuMetlib[[1]]
# # zhuMetlib.compound.pos <- zhuMetlib.compound[[1]]
# # zhuMetlib.compound.neg <- zhuMetlib.compound[[2]]
# #
# # zhuMetlib.meta <- zhuMetlib[[2]]
# # zhuMetlib.meta.compound <- zhuMetlib.meta[[1]]
# # zhuMetlib.meta.pos <- zhuMetlib.meta[[2]]
# # zhuMetlib.meta.neg <- zhuMetlib.meta[[3]]
# #
# #
# #
# #
# # instrument <- lapply(massbank, function(x){
# # x[[1]][9, 2]
# # })
# #
# # instrument <- unlist(instrument)
# #
# # ##only LC-ESI-QTOF, MALDI-TOFTOF, GC-EI-TOF, LC-ESI-ITTOF, ESI-ITTOF,APCI-ITTOF,LC-ESI-TOF
# # #MALDI-TOF, CE-ESI-TOF, ESI-QTOF are remained
# #
# # idx <- which(instrument %in% c("LC-ESI-QTOF",
# # "MALDI-TOFTOF", "GC-EI-TOF",
# # "LC-ESI-ITTOF", "ESI-ITTOF",
# # "APCI-ITTOF", "LC-ESI-TOF",
# # "MALDI-TOF", "CE-ESI-TOF", "ESI-QTOF"
# # ))
# #
# # massbank1 <- massbank[idx]
# #
# #
# #
# # polarity <- lapply(massbank1, function(x){
# # x[[1]][11, 2]
# # })
# #
# # polarity <- unlist(polarity)
# # massbank.pos <- massbank1[which(polarity == "POSITIVE")]
# # massbank.neg <- massbank1[which(polarity == "NEGATIVE")]
# #
# #
# # ce <- lapply(massbank1, function(x){
# # x[[1]][12, 2]
# # })
# #
# # ce <- unlist(ce)
# # table(ce)
# #
# # colnames(zhuMetlib.meta.compound)
# #
# # name <- unlist(lapply(massbank1, function(x){
# # x[[1]][1,2]
# # }))
# #
# # name <- unlist(lapply(strsplit(name, split = ';'), function(x) x[1]))
# #
# # formula <- unlist(lapply(massbank1, function(x){
# # x[[1]][2,2]
# # }))
# #
# # cas <- unlist(lapply(massbank1, function(x){
# # x[[1]][6,2]
# # }))
# #
# # pubchem <- unlist(lapply(massbank1, function(x){
# # x[[1]][7,2]
# # }))
# #
# # mz <- unlist(lapply(massbank1, function(x){
# # x[[1]][3,2]
# # }))
# #
# # mz <- as.numeric(mz)
# #
# # labid <- paste("MB", 1:length(massbank1), sep = "")
# #
# # hmdb <- rep(NA, length(mz))
# #
# # colnames(zhuMetlib.meta.compound)
# # meta.compound <- data.frame(labid, name, mz, formula, cas, hmdb, stringsAsFactors = FALSE)
# #
# # meta.pos <- data.frame(labid, mz, "10ppm", "qc1", stringsAsFactors = FALSE)[which(polarity == "POSITIVE"),]
# # colnames(meta.pos)[3:4] <- c("ppm", "qc")
# # meta.pos <- list(meta.pos)
# # names(meta.pos) <- "30"
# #
# # meta.neg <- data.frame(labid, mz, "10ppm", "qc1", stringsAsFactors = FALSE)[which(polarity == "NEGATIVE"),]
# # colnames(meta.neg)[3:4] <- c("ppm", "qc")
# # meta.neg <- list(meta.neg)
# # names(meta.neg) <- "30"
# #
# #
# #
# #
# # compound.pos <- lapply(massbank.pos, function(x) x[[2]])
# # compound.pos <- lapply(compound.pos, function(x){
# # colnames(x)[2] <- "intensity"
# # x <- list(x)
# # names(x) <- "30"
# # x
# # })
# #
# # names(compound.pos) <- labid[which(polarity == "POSITIVE")]
# #
# # names(zhuMetlib)
# #
# # compound.neg <- lapply(massbank.neg, function(x) x[[2]])
# # compound.neg <- lapply(compound.neg, function(x){
# # colnames(x)[2] <- "intensity"
# # x <- list(x)
# # names(x) <- "30"
# # x
# # })
# #
# # names(compound.neg) <- labid[which(polarity == "NEGATIVE")]
# # #
# # # zhuMetlib.compound <- zhuMetlib[[1]]
# # # zhuMetlib.compound.pos <- zhuMetlib.compound[[1]]
# # # zhuMetlib.compound.neg <- zhuMetlib.compound[[2]]
# # #
# # # zhuMetlib.meta <- zhuMetlib[[2]]
# # # zhuMetlib.meta.compound <- zhuMetlib.meta[[1]]
# # # zhuMetlib.meta.pos <- zhuMetlib.meta[[2]]
# # # zhuMetlib.meta.neg <- zhuMetlib.meta[[3]]
# #
# # compound <- list(compound.pos, compound.neg)
# # names(compound) <- c("pos", "neg")
# #
# # meta <- list(meta.compound, meta.pos, meta.neg)
# # names(meta) <- names(zhuMetlib.meta)
# #
# # massBankLib <- list(compound, meta)
# # names(massBankLib) <- names(zhuMetlib)
# #
# #
# # save(massBankLib, file = "massBankLib")
# #
# #
# # names(massBankLib)
# # names(zhuMetlib)
# #
# #
# # names(massBankLib[[1]])
# # names(zhuMetlib[[1]])
# #
# #
# # names(massBankLib[[1]][[1]])
# # names(zhuMetlib[[1]][[1]])
# #
# # names(massBankLib[[2]])
# # names(zhuMetlib[[2]])
# #
# # names(massBankLib[[2]][[1]])
# # names(zhuMetlib[[2]][[1]])
# #
# #
# # names(massBankLib[[2]][[2]])
# # names(zhuMetlib[[2]][[2]])
# #
# #
# # load("mz")
# #
# # cbind(massBankLib$meta$compound$mz, mz)
# #
# # temp.idx <- match(massBankLib$meta$compound$name[which(is.na(mz))],
# # unlist(lapply(massbank, function(x) strsplit(x$ms2.info[1,2], split = ";")[[1]][1])))
# #
# #
# #
# # mz[which(is.na(mz))] <-
# # as.numeric(unlist(lapply(massbank[temp.idx], function(x) x$ms2.info[3,2])))
# #
# #
# #
# # temp.idx.pos <- match(massBankLib$meta$pos$`30`$labid, massBankLib$meta$compound$labid)
# # temp.idx.neg <- match(massBankLib$meta$neg$`30`$labid, massBankLib$meta$compound$labid)
# #
# #
# # massBankLib$meta$pos$`30`$mz <- massBankLib$meta$compound$mz[temp.idx.pos]
# #
# # massBankLib$meta$neg$`30`$mz <- massBankLib$meta$compound$mz[temp.idx.neg]
# #
# # massBankLib$meta$compound$mz <- mz
# # save(massBankLib, file = "massBankLib")
# #
# #
# #
# #
# #
# #
# #
# #
#
# ###Massbank data
# setwd("D:/my github/metTools/data")
# load("massbank.rdata")
# instrument <- lapply(massbank, function(x){
# x[[1]][9, 2]
# })
#
# instrument <- unlist(instrument)
# table(instrument)
#
# ce <- unlist(lapply(massbank, function(x){
# x[[1]][12, 2]
# }))
#
# ##polarity
# polarity <- unlist(lapply(massbank, function(x){
# x[[1]][11, 2]
# }))
#
# table(polarity)
#
# massbank.pos <- massbank[which(polarity == "POSITIVE")]
# massbank.neg <- massbank[which(polarity == "NEGATIVE")]
#
# ##creat met.compound information
# names(zhuMetlib)
# zhuMetlib.compound <- zhuMetlib[[1]]
# zhuMetlib.compound.pos <- zhuMetlib.compound[[1]]
# zhuMetlib.compound.neg <- zhuMetlib.compound[[2]]
#
# zhuMetlib.meta <- zhuMetlib[[2]]
# zhuMetlib.meta.compound <- zhuMetlib.meta[[1]]
# zhuMetlib.meta.pos <- zhuMetlib.meta[[2]]
# zhuMetlib.meta.neg <- zhuMetlib.meta[[3]]
#
# colnames(zhuMetlib.meta.compound)
#
# name <- unlist(lapply(massbank, function(x){
# x[[1]][1,2]
# }))
#
# name <- unlist(lapply(strsplit(name, split = ';'), function(x) x[1]))
#
# formula <- unlist(lapply(massbank, function(x){
# x[[1]][2,2]
# }))
#
# cas <- unlist(lapply(massbank, function(x){
# x[[1]][6,2]
# }))
#
# pubchem <- unlist(lapply(massbank, function(x){
# x[[1]][7,2]
# }))
#
# mz <- unlist(lapply(massbank, function(x){
# x[[1]][3,2]
# }))
#
# mz <- as.numeric(mz)
#
# labid <- paste("MB", 1:length(massbank), sep = "")
#
# hmdb <- rep(NA, length(mz))
#
# massbank[[1]]$ms2.info$name
#
# colnames(zhuMetlib.meta.compound)
# smile <- unlist(lapply(massbank, function(x){
# x[[1]][4,2]
# }))
#
# iupac <- unlist(lapply(massbank, function(x){
# x[[1]][5,2]
# }))
#
# pubchem <- unlist(lapply(massbank, function(x){
# x[[1]][7,2]
# }))
#
#
# chemspider <- unlist(lapply(massbank, function(x){
# x[[1]][8,2]
# }))
#
# instrument.type <- unlist(lapply(massbank, function(x){
# x[[1]][9,2]
# }))
#
#
# instrument <- unlist(lapply(massbank, function(x){
# x[[1]][10,2]
# }))
#
#
# ce <- unlist(lapply(massbank, function(x){
# x[[1]][12,2]
# }))
#
#
# adduct <- unlist(lapply(massbank, function(x){
# x[[1]][14,2]
# }))
#
# precursor.mz <- adduct <- unlist(lapply(massbank, function(x){
# x[[1]][13,2]
# }))
#
#
# meta.compound <- data.frame(labid, name, mz, formula, cas, hmdb,
# smile, iupac, pubchem, chemspider,
# instrument.type, instrument, ce,
# adduct, precursor.mz,
# stringsAsFactors = FALSE)
#
# meta.pos <- data.frame(labid, mz, "10ppm", "qc1",
# stringsAsFactors = FALSE)[which(polarity == "POSITIVE"),]
# colnames(meta.pos)[3:4] <- c("ppm", "qc")
# meta.pos <- list(meta.pos)
# names(meta.pos) <- "30"
#
# meta.neg <- data.frame(labid, mz, "10ppm", "qc1", stringsAsFactors = FALSE)[which(polarity == "NEGATIVE"),]
# colnames(meta.neg)[3:4] <- c("ppm", "qc")
# meta.neg <- list(meta.neg)
# names(meta.neg) <- "30"
#
# compound.pos <- lapply(massbank.pos, function(x) x[[2]])
# compound.pos <- lapply(compound.pos, function(x){
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.pos) <- labid[which(polarity == "POSITIVE")]
#
# compound.neg <- lapply(massbank.neg, function(x) x[[2]])
# compound.neg <- lapply(compound.neg, function(x){
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.neg) <- labid[which(polarity == "NEGATIVE")]
#
#
# compound <- list(compound.pos, compound.neg)
# names(compound) <- c("pos", "neg")
#
# meta <- list(meta.compound, meta.pos, meta.neg)
# names(meta) <- names(zhuMetlib.meta)
#
# massBankLib <- list(compound, meta)
# names(massBankLib) <- names(zhuMetlib)
#
#
# save(massBankLib, file = "massBankLib.rda", compress = "xz")
#
#
# ####MoNA
# setwd("D:/study/database and library/MoNA/")
# mona_spec <- readMSP_MoNA(file = "D:/study/database and library/MoNA/MoNA-export-All_Spectra-msp/MoNA-export-All_Spectra.msp")
#
# save(mona_spec, file = "mona_spec", compress = "xz")
# # load("mona_spec")
# ##polarity
# polarity <- unlist(lapply(mona_spec, function(x){
# as.character(x[[1]]["Ion_mode", 1])
# }))
#
# table(polarity)
# ###peak with no polarity are removed
# mona_spec <- mona_spec[which(!is.na(polarity))]
# mona.pos <- mona_spec[which(polarity == "P")]
# mona.neg <- mona_spec[which(polarity == "N")]
#
# ##creat met.compound information
# names(zhuMetlib)
# zhuMetlib.compound <- zhuMetlib[[1]]
# zhuMetlib.compound.pos <- zhuMetlib.compound[[1]]
# zhuMetlib.compound.neg <- zhuMetlib.compound[[2]]
#
# zhuMetlib.meta <- zhuMetlib[[2]]
# zhuMetlib.meta.compound <- zhuMetlib.meta[[1]]
# zhuMetlib.meta.pos <- zhuMetlib.meta[[2]]
# zhuMetlib.meta.neg <- zhuMetlib.meta[[3]]
#
# colnames(zhuMetlib.meta.compound)
#
# name <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Name",1]
# }))
# sum(is.na(name))
# temp.idx1 <- which(!is.na(name))
# # name <- unlist(lapply(strsplit(name, split = ';'), function(x) x[1]))
#
# formula <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Formula",1]
# }))
#
# sum(is.na(formula))
# temp.idx2 <- which(!is.na(formula))
#
#
#
# cas <- rep(NA, length(mona_spec))
#
# pubchem <- rep(NA, length(mona_spec))
#
# mz <- unlist(lapply(mona_spec, function(x){
# x[[1]]["ExactMass",1]
# }))
#
# mz <- as.numeric(mz)
# temp.idx3 <- which(!is.na(mz))
#
# hmdb <- rep(NA, length(mona_spec))
#
# temp.idx <- intersect(intersect(temp.idx1, temp.idx2), temp.idx3)
#
# mona_spec <- mona_spec[temp.idx]
# labid <- paste("MONA", 1:length(mona_spec), sep = "")
#
# ##polarity
# polarity <- unlist(lapply(mona_spec, function(x){
# as.character(x[[1]]["Ion_mode", 1])
# }))
#
# table(polarity)
#
# mona.pos <- mona_spec[which(polarity == "P")]
# mona.neg <- mona_spec[which(polarity == "N")]
#
#
# name <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Name",1]
# }))
# sum(is.na(name))
#
# formula <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Formula",1]
# }))
#
# sum(is.na(formula))
#
# cas <- rep(NA, length(mona_spec))
#
# smile <- rep(NA, length(mona_spec))
#
# pubchem <- rep(NA, length(mona_spec))
#
# mz <- unlist(lapply(mona_spec, function(x){
# x[[1]]["ExactMass",1]
# }))
#
# mz <- as.numeric(mz)
#
# hmdb <- rep(NA, length(mona_spec))
#
# rownames(mona_spec[[1]]$info)
#
# colnames(zhuMetlib.meta.compound)
#
# InChIKey <- unlist(lapply(mona_spec, function(x){
# as.character(x[[1]]["InChIKey",1])
# }))
#
#
# instrument.type <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Instrument_type",1]
# }))
#
#
# instrument <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Instrument",1]
# }))
#
#
# ce <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Collision_energy",1]
# }))
#
#
# adduct <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Precursor_type",1]
# }))
#
#
# comment <- unlist(lapply(mona_spec, function(x){
# x[[1]]["Comments",1]
# }))
#
# precursor.mz <- unlist(lapply(mona_spec, function(x){
# x[[1]]["PrecursorMZ",1]
# }))
#
#
# meta.compound <- data.frame(labid, name, mz, formula, cas, hmdb,
# smile, adduct,
# instrument.type, instrument, ce,
# adduct, precursor.mz, comment,
# stringsAsFactors = FALSE)
#
# meta.pos <- data.frame(labid, mz, "10ppm", "qc1",
# stringsAsFactors = FALSE)[which(polarity == "P"),]
# colnames(meta.pos)[3:4] <- c("ppm", "qc")
# meta.pos <- list(meta.pos)
# names(meta.pos) <- "30"
#
# meta.neg <- data.frame(labid, mz, "10ppm", "qc1",
# stringsAsFactors = FALSE)[which(polarity == "N"),]
# colnames(meta.neg)[3:4] <- c("ppm", "qc")
# meta.neg <- list(meta.neg)
# names(meta.neg) <- "30"
#
# compound.pos <- lapply(mona.pos, function(x) x[[2]])
# compound.pos <- lapply(compound.pos, function(x){
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.pos) <- labid[which(polarity == "P")]
#
# compound.neg <- lapply(mona.neg, function(x) x[[2]])
# compound.neg <- lapply(compound.neg, function(x){
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.neg) <- labid[which(polarity == "N")]
#
#
# compound <- list(compound.pos, compound.neg)
# names(compound) <- c("pos", "neg")
#
# meta <- list(meta.compound, meta.pos, meta.neg)
# names(meta) <- names(zhuMetlib.meta)
#
# monaLib <- list(compound, meta)
# names(monaLib) <- names(zhuMetlib)
#
#
# save(monaLib, file = "monaLib.rda", compress = "xz")
#
#
#
#
# ###metlin
# setwd("D:/study/database and library/metlin")
# load("metlinlib.rdata")
# names(metlinlib)
# metlinLib <- metlinlib[[1]]
# names(metlinLib)
#
# head(metlinLib$meta$compound)
#
# temp.pos <- mapply(function(x,y){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# },
# x = metlinLib$compound$pos,
# y = names(metlinLib$compound$pos))
#
# temp.pos <- do.call(what = c, args = temp.pos)
#
# names(temp.pos) <- unlist(lapply(stringr::str_split(string = names(temp.pos), pattern = "\\."), function(x){
# x[2]
# }))
#
#
#
#
# temp.neg <- mapply(function(x,y){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# },
# x = metlinLib$compound$neg,
# y = names(metlinLib$compound$neg))
#
# temp.neg <- do.call(what = c, args = temp.neg)
#
# names(temp.neg) <- unlist(lapply(stringr::str_split(string = names(temp.neg), pattern = "\\."), function(x){
# x[2]
# }))
#
#
# temp.name <- unique(c(names(temp.pos), names(temp.neg)))
#
#
# temp.compound <- metlinLib$meta$compound
#
# temp.compound <- apply(temp.compound, 1, function(x){
# x <- t(data.frame(x))
# x <- as.data.frame(x)
# new.id <- grep(pattern = x[1,1], x = temp.name, value = TRUE)
# x <- x[rep(1, length(new.id)),]
# x$labid <- new.id
# rownames(x) <- NULL
# x
# })
#
# temp.compound <- do.call(rbind, temp.compound)
#
# rownames(temp.compound) <- NULL
#
# names(metlinLib$meta$pos)
#
#
# temp.meta.pos <- metlinLib$meta$pos
# temp.meta.neg <- metlinLib$meta$neg
#
# temp.meta.pos <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.pos,
# y = names(temp.meta.pos))
#
# temp.meta.neg <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.neg,
# y = names(temp.meta.neg))
#
#
# temp.meta.pos <- do.call(rbind, args = temp.meta.pos)
# temp.meta.neg <- do.call(rbind, args = temp.meta.neg)
#
# rownames(temp.meta.pos) <- NULL
# rownames(temp.meta.neg) <- NULL
#
#
# length(temp.pos)
# dim(temp.meta.pos)
#
# length(temp.neg)
# dim(temp.meta.neg)
#
# temp.pos <- lapply(temp.pos, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.neg <- lapply(temp.neg, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.meta.pos <- list(temp.meta.pos)
# names(temp.meta.pos) <- "30"
#
# temp.meta.neg <- list(temp.meta.neg)
# names(temp.meta.neg) <- "30"
#
# metlinLib$compound$pos <- temp.pos
# metlinLib$compound$neg <- temp.neg
#
# metlinLib$meta$compound <- temp.compound
# metlinLib$meta$pos <- temp.meta.pos
# metlinLib$meta$neg <- temp.meta.neg
#
# save(metlinLib, file = "metlibLib.rda", compress = "xz")
#
#
# ##zhu_nist
# setwd("D:/study/database and library/zhu_nist")
# load("zhuMetlib.rda")
# names(zhuMetlib)
# nistLib <- zhuMetlib
# names(nistLib)
#
# head(nistLib$meta$compound)
#
#
#
# temp.pos <- mapply(function(x,y){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# },
# x = nistLib$compound$pos,
# y = names(nistLib$compound$pos))
#
# temp.pos <- do.call(what = c, args = temp.pos)
#
# names(temp.pos) <- unlist(lapply(stringr::str_split(string = names(temp.pos), pattern = "\\."), function(x){
# x[2]
# }))
#
#
# # for(i in 1:length(nistLib$compound$neg)){
# # cat(i, " ")
# # x <- nistLib$compound$neg[[i]]
# # y <- names(nistLib$compound$neg)[i]
# # if(length(x) != 0){
# # names(x) <- stringr::str_c(y, names(x), sep = "_")
# # }
# #
# # }
#
# temp.neg <- mapply(function(x,y){
# if(length(x) != 0){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# }
# },
# x = nistLib$compound$neg,
# y = names(nistLib$compound$neg))
#
# temp.neg <- do.call(what = c, args = temp.neg)
#
# names(temp.neg) <- unlist(lapply(stringr::str_split(string = names(temp.neg), pattern = "\\."), function(x){
# x[2]
# }))
#
#
# temp.name <- unique(c(names(temp.pos), names(temp.neg)))
#
#
# temp.compound <- nistLib$meta$compound
#
# temp.compound <- apply(temp.compound, 1, function(x){
# x <- t(data.frame(x))
# x <- as.data.frame(x)
# new.id <- grep(pattern = x[1,1], x = temp.name, value = TRUE)
# x <- x[rep(1, length(new.id)),]
# x$labid <- new.id
# rownames(x) <- NULL
# x
# })
#
# temp.compound <- do.call(rbind, temp.compound)
#
# rownames(temp.compound) <- NULL
#
# names(nistLib$meta$pos)
#
#
# temp.meta.pos <- nistLib$meta$pos
# temp.meta.neg <- nistLib$meta$neg
#
# temp.meta.pos <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.pos,
# y = names(temp.meta.pos))
#
# temp.meta.neg <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.neg,
# y = names(temp.meta.neg))
#
#
# temp.meta.pos <- do.call(rbind, args = temp.meta.pos)
# temp.meta.neg <- do.call(rbind, args = temp.meta.neg)
#
# rownames(temp.meta.pos) <- NULL
# rownames(temp.meta.neg) <- NULL
#
#
# length(temp.pos)
# dim(temp.meta.pos)
#
# length(temp.neg)
# dim(temp.meta.neg)
#
# temp.pos <- lapply(temp.pos, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.neg <- lapply(temp.neg, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.meta.pos <- list(temp.meta.pos)
# names(temp.meta.pos) <- "30"
#
# temp.meta.neg <- list(temp.meta.neg)
# names(temp.meta.neg) <- "30"
#
# nistLib$compound$pos <- temp.pos
# nistLib$compound$neg <- temp.neg
#
# nistLib$meta$compound <- temp.compound
# nistLib$meta$pos <- temp.meta.pos
# nistLib$meta$neg <- temp.meta.neg
#
# save(nistLib, file = "nistLib.rda", compress = "xz")
#
#
#
# ###orbitrap
# setwd("D:/study/database and library/nist_orbitrap")
# load("orbitrapMetlib.rda")
# names(orbitrapMetlib)
# orbitrapLib <- orbitrapMetlib
# names(orbitrapLib)
#
# head(orbitrapLib$meta$compound)
#
#
#
# temp.pos <- mapply(function(x,y){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# },
# x = orbitrapLib$compound$pos,
# y = names(orbitrapLib$compound$pos))
#
# temp.pos <- do.call(what = c, args = temp.pos)
#
# names(temp.pos) <- unlist(lapply(stringr::str_split(string = names(temp.pos), pattern = "\\."), function(x){
# x[2]
# }))
#
#
# # for(i in 1:length(orbitrapLib$compound$neg)){
# # cat(i, " ")
# # x <- orbitrapLib$compound$neg[[i]]
# # y <- names(orbitrapLib$compound$neg)[i]
# # if(length(x) != 0){
# # names(x) <- stringr::str_c(y, names(x), sep = "_")
# # }
# #
# # }
#
# temp.neg <- mapply(function(x,y){
# if(length(x) != 0){
# names(x) <- stringr::str_c(y, names(x), sep = "_")
# x
# }
# },
# x = orbitrapLib$compound$neg,
# y = names(orbitrapLib$compound$neg))
#
# temp.neg <- do.call(what = c, args = temp.neg)
#
# names(temp.neg) <- unlist(lapply(stringr::str_split(string = names(temp.neg), pattern = "\\."), function(x){
# x[2]
# }))
#
#
# temp.name <- unique(c(names(temp.pos), names(temp.neg)))
#
#
# temp.compound <- orbitrapLib$meta$compound
#
# temp.compound <- apply(temp.compound, 1, function(x){
# x <- t(data.frame(x))
# x <- as.data.frame(x)
# new.id <- grep(pattern = x[1,1], x = temp.name, value = TRUE)
# x <- x[rep(1, length(new.id)),]
# x$labid <- new.id
# rownames(x) <- NULL
# x
# })
#
# temp.compound <- do.call(rbind, temp.compound)
#
# rownames(temp.compound) <- NULL
#
# names(orbitrapLib$meta$pos)
#
#
# temp.meta.pos <- orbitrapLib$meta$pos
# temp.meta.neg <- orbitrapLib$meta$neg
#
# temp.meta.pos <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.pos,
# y = names(temp.meta.pos))
#
# temp.meta.neg <- mapply(function(x,y){
# x$labid <- stringr::str_c(x$labid, y, sep = "_")
# list(x)
# },
# x = temp.meta.neg,
# y = names(temp.meta.neg))
#
#
# temp.meta.pos <- do.call(rbind, args = temp.meta.pos)
# temp.meta.neg <- do.call(rbind, args = temp.meta.neg)
#
# rownames(temp.meta.pos) <- NULL
# rownames(temp.meta.neg) <- NULL
#
#
# length(temp.pos)
# dim(temp.meta.pos)
#
# length(temp.neg)
# dim(temp.meta.neg)
#
# temp.pos <- lapply(temp.pos, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.neg <- lapply(temp.neg, function(x){
# x <- list(x)
# names(x) <- "30"
# x
# })
#
#
# temp.meta.pos <- list(temp.meta.pos)
# names(temp.meta.pos) <- "30"
#
# temp.meta.neg <- list(temp.meta.neg)
# names(temp.meta.neg) <- "30"
#
# orbitrapLib$compound$pos <- temp.pos
# orbitrapLib$compound$neg <- temp.neg
#
# orbitrapLib$meta$compound <- temp.compound
# orbitrapLib$meta$pos <- temp.meta.pos
# orbitrapLib$meta$neg <- temp.meta.neg
#
# save(orbitrapLib, file = "orbitrapLib.rda", compress = "xz")
#
#
# ###HMDB
# setwd("D:/study/database and library/HMDB/hmdb_experimental_msms_spectra")
# library(XML)
# library("methods")
#
# file <- dir()
# hmdbLib <- vector(mode = "list", length = length(file))
# for(i in 1:length(file)){
# cat(i, " ")
# temp.file <- file[i]
# result <- xmlParse(file = temp.file)
# rootnode <- xmlRoot(result)
# info <- xmlSApply(rootnode, function(x) xmlSApply(x, xmlValue))
# names(info) <- unname(names(rootnode))
# info <- lapply(info, unname)
# ms2.mz <- sapply(getNodeSet(doc = rootnode[[26]], path = "//mass-charge"), xmlValue)
# ms2.int <- sapply(getNodeSet(doc = rootnode[[26]], path = "//intensity"), xmlValue)
# ms2 <- data.frame("mz" = ms2.mz, "intensity" = ms2.int,
# stringsAsFactors = FALSE)
# info[[26]] <- ms2
#
# ms2.info <- info[c(10, 17, 18, 24, 25)]
# ms2.info <- lapply(ms2.info, function(x){
# if(length(x) == 0){
# x <- NA
# }
# x
# })
# ms2.spec <- info[[26]]
#
# ms2.info <- do.call(rbind, ms2.info)
# ms2.info <- data.frame("name" = rownames(ms2.info), "value" = ms2.info[,1],
# stringsAsFactors = FALSE)
# ms2.info <- tibble::as_tibble(ms2.info)
#
# temp.spec <- list(ms2.info = ms2.info, ms2.spec = ms2.spec)
# hmdbLib[[i]] <- temp.spec
#
# }
#
# hmdb <- hmdbLib
# save(hmdb, file = "hmdb")
# load("hmdb")
# ##polarity
# polarity <- unlist(lapply(hmdb, function(x){
# x[[1]][3, 2]
# }))
#
# temp.idx1 <- which(polarity != "N/A")
#
# table(polarity)
#
# hmdb <- hmdb[temp.idx1]
#
# polarity <- unlist(lapply(hmdb, function(x){
# x[[1]][3, 2]
# }))
#
# polarity <- stringr::str_to_lower(polarity)
#
# instrument <- lapply(hmdb, function(x){
# x[[1]][1, 2]
# })
#
# instrument <- unlist(instrument)
# table(instrument)
#
# ce <- unlist(lapply(hmdb, function(x){
# x[[1]][2, 2]
# }))
#
# sum(is.na(ce))
#
#
#
# ##creat met.compound information
# names(zhuMetlib)
# zhuMetlib.compound <- zhuMetlib[[1]]
# zhuMetlib.compound.pos <- zhuMetlib.compound[[1]]
# zhuMetlib.compound.neg <- zhuMetlib.compound[[2]]
#
# zhuMetlib.meta <- zhuMetlib[[2]]
# zhuMetlib.meta.compound <- zhuMetlib.meta[[1]]
# zhuMetlib.meta.pos <- zhuMetlib.meta[[2]]
# zhuMetlib.meta.neg <- zhuMetlib.meta[[3]]
#
# colnames(zhuMetlib.meta.compound)
#
# hmdb.id <- unlist(lapply(hmdb, function(x){
# x[[1]][4,2]
# }))
#
# hmdb.id <- unname(hmdb.id)
# hmdb.id <- stringr::str_replace(string = hmdb.id, pattern = "00", replacement = "")
#
#
# load("G:/Project/MetDNA/annotation and identification/annotation/HMDB compound database/hmdbAllinf.rda")
#
# name <- as.character(hmdbAllinf$Name[match(hmdb.id, hmdbAllinf$HMDBID)])
# sum(is.na(name))
#
#
# formula <- as.character(hmdbAllinf$Formula[match(hmdb.id, hmdbAllinf$HMDBID)])
#
# cas <- as.character(hmdbAllinf$CAS_Registry_Number[match(hmdb.id, hmdbAllinf$HMDBID)])
#
# pubchem <- rep(NA, length(name))
# cas <- as.character(hmdbAllinf$CAS_Registry_Number[match(hmdb.id, hmdbAllinf$HMDBID)])
#
#
# mz <- as.character(hmdbAllinf$MonoisotopicMass[match(hmdb.id, hmdbAllinf$HMDBID)])
#
# mz <- as.numeric(mz)
#
# labid <- paste("HM", 1:length(hmdb), sep = "")
#
# # hmdb.id <- rep(NA, length(mz))
#
# hmdb[[1]]$ms2.info$name
#
# colnames(zhuMetlib.meta.compound)
#
# metlinid <- as.character(hmdbAllinf$MetlinID[match(hmdb.id, hmdbAllinf$HMDBID)])
#
#
# keggid <- as.character(hmdbAllinf$KEGGID[match(hmdb.id, hmdbAllinf$HMDBID)])
#
# smpdbid <- as.character(hmdbAllinf$SMPDB_ID[match(hmdb.id, hmdbAllinf$HMDBID)])
# smile <- as.character(hmdbAllinf$Smiles[match(hmdb.id, hmdbAllinf$HMDBID)])
#
# InChiKey <- as.character(hmdbAllinf$InChiKey[match(hmdb.id, hmdbAllinf$HMDBID)])
# ChemSpider_ID <- as.character(hmdbAllinf$ChemSpider_ID[match(hmdb.id, hmdbAllinf$HMDBID)])
#
#
# meta.compound <- data.frame(labid, name, mz, formula, cas, hmdb.id,
# smile, ChemSpider_ID, metlinid, keggid, smpdbid,
# instrument, ce,InChiKey,
# stringsAsFactors = FALSE)
# meta.compound <- meta.compound[which(!is.na(name) & !is.na(mz) & !is.na(formula)),]
#
# polarity <- polarity[which(!is.na(name) & !is.na(mz) & !is.na(formula))]
#
# hmdb.pos <- hmdb[which(polarity == "positive")]
# hmdb.neg <- hmdb[which(polarity == "negative")]
#
# meta.pos <- data.frame(
# "labid" = meta.compound$labid,
# "mz" = meta.compound$mz,
# "10ppm", "qc1",
# stringsAsFactors = FALSE)[which(polarity == "positive"),]
# colnames(meta.pos)[3:4] <- c("ppm", "qc")
# meta.pos <- list(meta.pos)
# names(meta.pos) <- "30"
#
# meta.neg <- data.frame(
# "labid" = meta.compound$labid,
# "mz" = meta.compound$mz,
# "10ppm", "qc1",
# stringsAsFactors = FALSE)[which(polarity == "negative"),]
#
# colnames(meta.neg)[3:4] <- c("ppm", "qc")
# meta.neg <- list(meta.neg)
# names(meta.neg) <- "30"
#
# compound.pos <- lapply(hmdb.pos, function(x) x[[2]])
#
#
#
# compound.pos <- lapply(compound.pos, function(x){
# if(nrow(x) == 0) return(NA)
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.pos) <- labid[which(polarity == "positive")]
#
# temp.idx.pos <- which(!unlist(lapply(compound.pos, is.na)))
# compound.pos <- compound.pos[temp.idx.pos]
#
# compound.neg <- lapply(hmdb.neg, function(x) x[[2]])
# compound.neg <- lapply(compound.neg, function(x){
# colnames(x)[2] <- "intensity"
# x <- list(x)
# names(x) <- "30"
# x
# })
#
# names(compound.neg) <- labid[which(polarity == "negative")]
#
#
# compound <- list(compound.pos, compound.neg)
# names(compound) <- c("pos", "neg")
#
# meta <- list(meta.compound, meta.pos, meta.neg)
# names(meta) <- names(zhuMetlib.meta)
#
# hmdbLib <- list(compound, meta)
# names(hmdbLib) <- names(zhuMetlib)
#
#
# save(hmdbLib, file = "hmdbLib.rda", compress = "xz")
#
#
#
#
# library(magrittr)
#
# names(hmdbDatabase0.0.1@spectra.data$Spectra.positive) %in% hmdbDatabase0.0.1@spectra.info$Lab.ID %>%
# which(.) %>%
# `[` (hmdbDatabase0.0.1@spectra.info$HMDB.ID, .) %>%
# unique(.) %>%
# length
#
#
# names(hmdbDatabase0.0.1@spectra.data$Spectra.negative) %in% hmdbDatabase0.0.1@spectra.info$Lab.ID %>%
# which(.) %>%
# `[` (hmdbDatabase0.0.1@spectra.info$HMDB.ID, .) %>%
# unique(.) %>%
# length
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