Nothing
R/MSimport.R
In erah: Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics
Defines functions
importMSP
importGMD
list.DB
get.compound.info_MSP
get.compound.info_GMD
Documented in
importGMD
importMSP
get.compound.info_GMD <- function(k, Spl.List, type)
{
#kmain <<-k
x <- Spl.List[[k]]
x.split <- unlist(apply(as.matrix(x),1, function(x) {strsplit(x,":")[[1]]}), recursive=T)
Name=" "
Synon=" "
RI.VAR5.FAME=0
RI.VAR5.ALK=0
RI.MDN35.FAME=0
RI.MDN35.ALK=0
CAS=" "
Formula=" "
InChi=" "
KEGG=""
MW=0
Comment=" "
GMD.LINK=" "
GMD.VERS=" "
Spectra <- ""
Caps <- apply(as.matrix(x),1, function(x) {strsplit(x,":")[[1]]})
Sp.Ini <- which(lapply(Caps,function(y)y[1])=="Num Peaks")
Spectra <- paste(x[(Sp.Ini+1):length(x)],collapse="")
for(j in 1:length(x.split))
{
if(x.split[j]==" MST N") Name=x.split[j+1]
if(x.split[j]==" METB N") {
if(Synon!=" ") Synon=paste(Synon, "//", x.split[j+1], sep=" ")
if(Synon==" ") Synon = x.split[j+1]
}
if(x.split[j]==" RI")
{
if(type=="MDN35.ALK") RI.MDN35.ALK=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="MDN35.FAME") RI.MDN35.FAME=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="VAR5.ALK") RI.VAR5.ALK=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="VAR5.FAME") RI.VAR5.FAME=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
}
if(x.split[j]==" MST SEL MASS") SelMZ <- as.vector(sapply(strsplit(x.split[j+1], "\\|")[[1]],function(z){
if (grepl('NA',z)) {
return(NA)
} else {
return(as.numeric(z))
}
}))
if(x.split[j]=="CAS#") CAS=x.split[j+1]
if(x.split[j]=="Formula") Formula=x.split[j+1]
if(x.split[j]==" METB InChI") InChi= strsplit(x.split[j+1], "=")[[1]][2]
if(x.split[j]==" METB KEGG") KEGG=x.split[j+1]
if(x.split[j]=="MW")
{
no.dot <- apply(as.matrix(x.split[j+1]), 2, gsub, patt="\\.", replace="")
MW=as.numeric(apply(as.matrix(no.dot), 2, gsub, patt=",", replace="."))
}
if(x.split[j]=="Comment") Comment=x.split[j+1]
if(x.split[j]==" GMD LINK") GMD.LINK=paste(x.split[j+1],":",x.split[j+2],sep="")
if(x.split[j]==" GMD VERS") GMD.VERS= paste(x.split[j+1],":",x.split[j+2],sep="")
}
#cat(Name, "\n")
s.spl <- strsplit(Name," ")[[1]]; Name <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Synon," ")[[1]]; Synon <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(CAS," ")[[1]]; CAS <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Formula," ")[[1]]; Formula <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(KEGG," ")[[1]]; KEGG <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Comment," ")[[1]]; Comment <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(GMD.LINK," ")[[1]]; GMD.LINK <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(GMD.VERS," ")[[1]]; GMD.VERS <- paste(s.spl[-1], collapse=" ")
compound.info <- list(Name=Name, Synon=Synon, RI.VAR5.FAME=RI.VAR5.FAME, RI.VAR5.ALK=RI.VAR5.ALK, RI.MDN35.FAME=RI.MDN35.FAME, RI.MDN35.ALK=RI.MDN35.ALK, SelMZ=SelMZ, CAS=CAS, InChi=InChi, Formula=Formula, MW=MW, KEGG=KEGG, Comment=Comment, GMD.LINK=GMD.LINK, GMD.VERS=GMD.VERS, Spectra=Spectra)
compound.info
}
get.compound.info_MSP <- function(k, Spl.List, type)
{
#kmain <<-k
x <- Spl.List[[k]]
x.split <- unlist(apply(as.matrix(x),1, function(x) {strsplit(x,":")[[1]]}), recursive=T)
Name=" "
Synon=" "
RI.VAR5.FAME=0
RI.VAR5.ALK=0
RI.MDN35.FAME=0
RI.MDN35.ALK=0
CAS=" "
Formula=" "
InChi=" "
KEGG=""
MW=0
Comment=" "
GMD.LINK=" "
GMD.VERS=" "
SelMZ=NA
Spectra <- ""
Caps <- apply(as.matrix(x),1, function(x) {strsplit(x,":")[[1]]})
Sp.Ini <- which(lapply(Caps,function(y)y[1])=="Num Peaks" | lapply(Caps,function(y)y[1])=="Num peaks")
Spectra.semicolon <- paste(x[(Sp.Ini+1):length(x)],collapse="")
Spectra.semicolon <- gsub(' {2,}', ' ', Spectra.semicolon)
if(strsplit(Spectra.semicolon, '')[[1]][1]==' ') Spectra.semicolon <- paste(strsplit(Spectra.semicolon, '')[[1]][-1], collapse='')
if(length(grep(";", Spectra.semicolon))!=0){
Spectra.dot <- sapply(strsplit(Spectra.semicolon, ";")[[1]], function(y) paste(strsplit(y, " ")[[1]], collapse=":"))
}else{
Spectra.dot <- sapply(x[(Sp.Ini+1):length(x)], function(y) paste(strsplit(y, " ")[[1]], collapse=":"))
}
Spectra.dot <- sapply(Spectra.dot, function(y) {
yV <- y
nVs <- strsplit(y[1], '')[[1]] %in% c(0:9)
if(nVs[1]==FALSE) yV <- paste(strsplit(y, '')[[1]][-1], collapse='')
if(nVs[length(nVs)]==FALSE) yV <- paste(strsplit(y, '')[[1]][-length(nVs)], collapse='')
yV
})
Spectra <- paste(Spectra.dot , collapse=" ")
for(j in 1:length(x.split))
{
if(x.split[j]=="Name") Name=x.split[j+1]
#if(x.split[j]==" MST SEL MASS") SelMZ <- as.vector(sapply(strsplit(x.split[j+1], "\\|"), as.numeric))
if(x.split[j]=="CAS#" | x.split[j]=="CASNO") CAS=x.split[j+1]
if(x.split[j]=="Formula") Formula=x.split[j+1]
if(x.split[j]=="DB#") InChi= x.split[j+1]
#if(x.split[j]==" METB KEGG") KEGG=x.split[j+1]
if(x.split[j]=="RI")
{
if(type=="MDN35.ALK") RI.MDN35.ALK=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="MDN35.FAME") RI.MDN35.FAME=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="VAR5.ALK") RI.VAR5.ALK=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="VAR5.FAME") RI.VAR5.FAME=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
}
if(x.split[j]=="MW")
{
no.dot <- apply(as.matrix(x.split[j+1]), 2, gsub, patt="\\.", replace="")
MW=as.numeric(apply(as.matrix(no.dot), 2, gsub, patt=",", replace="."))
}
if(x.split[j]=="Comments" | x.split[j]=="Comment") Comment=x.split[j+1]
#if(x.split[j]==" GMD LINK") GMD.LINK=paste(x.split[j+1],":",x.split[j+2],sep="")
#if(x.split[j]==" GMD VERS") GMD.VERS= paste(x.split[j+1],":",x.split[j+2],sep="")
}
#cat(Name, "\n")
s.spl <- strsplit(Name," ")[[1]]; Name <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Synon," ")[[1]]; Synon <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(CAS," ")[[1]]; CAS <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Formula," ")[[1]]; Formula <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(KEGG," ")[[1]]; KEGG <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Comment," ")[[1]]; Comment <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(GMD.LINK," ")[[1]]; GMD.LINK <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(GMD.VERS," ")[[1]]; GMD.VERS <- paste(s.spl[-1], collapse=" ")
compound.info <- list(Name=Name, Synon=Synon, RI.VAR5.FAME=RI.VAR5.FAME, RI.VAR5.ALK=RI.VAR5.ALK, RI.MDN35.FAME=RI.MDN35.FAME, RI.MDN35.ALK=RI.MDN35.ALK, SelMZ=SelMZ, CAS=CAS, InChi=InChi, Formula=Formula, MW=MW, KEGG=KEGG, Comment=Comment, GMD.LINK=GMD.LINK, GMD.VERS=GMD.VERS, Spectra=Spectra)
compound.info
}
list.DB <- function(DB.object)
{
k <- 1
Cont <- 1
Spl.List <- list()
for(i in 1:length(DB.object))
{
if(DB.object[i]=="")
{
Spl.List[Cont] <- list(Compound=DB.object[k:(i-1)])
k <- i + 1
Cont <- Cont + 1
}
}
Spl.List
}
#' @name importGMD
#' @aliases importGMD
#' @title Import MSP files from GMD to R
#' @description Import the Golm Metabolome Database.
#' @usage importGMD(filename, DB.name, DB.version, DB.info,
#' type = c("VAR5.ALK","VAR5.FAME","MDN35.ALK", "MDN35.FAME"))
#' @param filename The filepath containing the GMD database file.
#' @param DB.name The name of the database (each user may chose its own name
#' @param DB.version The version of the database (each user may chose its own version)
#' @param DB.info Some info about the database for further reference
#' @param type The type of RI to be imported from the database
#' @details For more details, please see the eRah manual
#' @export
importGMD <- function(filename, DB.name, DB.version, DB.info, type=c("VAR5.ALK","VAR5.FAME","MDN35.ALK", "MDN35.FAME"))
{
DB.MSP <- readLines(filename)
Spl.List <- list.DB(DB.MSP)
import.database <- list()
import.database <- lapply(1:length(Spl.List), function(x) get.compound.info_GMD(x, Spl.List, type))
final.database <- new("eRah_DB", name=DB.name, version=DB.version, info=DB.info, database=import.database)
final.database
}
#' @name importMSP
#' @aliases importMSP
#' @title Import MSP files to R
#' @description Import MS libraries in MSP format to eRah DB format.
#' @usage importMSP(filename, DB.name, DB.version, DB.info)
#' @param filename The filepath containing the MSP library file.
#' @param DB.name The name of the database (each user may chose its own name)
#' @param DB.version The version of the database (each user may chose its own version)
#' @param DB.info Some info about the database for further reference
#' @details
#' The MSP input file should look like:
#'
#' -----
#'
#' Name: Metabolite_name
#'
#' Formula: H2O
#'
#' MW: 666
#'
#' ExactMass: 666.266106
#'
#' CAS#: 11-22-3
#'
#' DB#: 1
#'
#' Comments: Metabolite_name reference standard
#'
#' Num Peaks: XX
#'
#' 53 1; 54 2; 55 5; 56 2; 57 2;
#'
#' 58 14; 59 18; 60 1000; 61 2; 67 1;
#'
#' Name: Metabolite_name_2
#'
#' Formula: H2O2
#'
#' MW: 999
#'
#' ExactMass: 999.266106
#'
#' CAS#: 22-33-4
#'
#' DB#: 2
#'
#'Comments: Metabolite_name_"" reference standard
#'
#' Num Peaks: XX
#'
#' 66 10; 67 1000; 155 560; 156 800; 157 2;
#'
#'158 14; 159 1; 160 100; 161 2; 167 1;
#'
#' -------
#'
#' OR
#'
#' -----
#'
#' Name: Metabolite_name
#'
#' Formula: H2O
#'
#' MW: 666
#'
#' ExactMass: 666.266106
#'
#' CASNO: 11-22-3
#'
#' DB#: 1
#'
#' Comment: Metabolite_name reference standard
#'
#' Num peaks: XX
#'
#' 53 1
#'
#' 54 2
#'
#' 55 5
#'
#' Name: Metabolite_name_2
#'
#' Formula: H2O2
#'
#' MW: 999
#'
#' ExactMass: 999.266106
#'
#' CASNO: 22-33-4
#'
#' DB#: 2
#'
#' Comment: Metabolite_name_"" reference standard
#'
#' Num Peaks: XX
#'
#' 66 10
#'
#' 67 1000
#'
#' 155 560
#'
#' -------
#'
#' Or combinations of both.
#'
#'
#' For more details, please see the eRah manual.
#' @export
#' @importFrom methods new
importMSP <- function(filename, DB.name, DB.version, DB.info)
{
DB.MSP <- readLines(filename)
Spl.List <- list.DB(DB.MSP)
import.database <- list()
OutFromList <- unlist(lapply(Spl.List, function(x) all(unlist(x)=="")))
Spl.List <- Spl.List[!OutFromList]
import.database <- lapply(1:length(Spl.List), function(x) get.compound.info_MSP(x, Spl.List, type="VAR5.ALK"))
final.database <- new("eRah_DB", name=DB.name, version=DB.version, info=DB.info, database=import.database)
final.database
}
Try the erah package in your browser
Any scripts or data that you put into this service are public.
erah documentation built on June 22, 2024, 11:01 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions importMSP importGMD list.DB get.compound.info_MSP get.compound.info_GMD
Documented in importGMD importMSP
get.compound.info_GMD <- function(k, Spl.List, type)
{
#kmain <<-k
x <- Spl.List[[k]]
x.split <- unlist(apply(as.matrix(x),1, function(x) {strsplit(x,":")[[1]]}), recursive=T)
Name=" "
Synon=" "
RI.VAR5.FAME=0
RI.VAR5.ALK=0
RI.MDN35.FAME=0
RI.MDN35.ALK=0
CAS=" "
Formula=" "
InChi=" "
KEGG=""
MW=0
Comment=" "
GMD.LINK=" "
GMD.VERS=" "
Spectra <- ""
Caps <- apply(as.matrix(x),1, function(x) {strsplit(x,":")[[1]]})
Sp.Ini <- which(lapply(Caps,function(y)y[1])=="Num Peaks")
Spectra <- paste(x[(Sp.Ini+1):length(x)],collapse="")
for(j in 1:length(x.split))
{
if(x.split[j]==" MST N") Name=x.split[j+1]
if(x.split[j]==" METB N") {
if(Synon!=" ") Synon=paste(Synon, "//", x.split[j+1], sep=" ")
if(Synon==" ") Synon = x.split[j+1]
}
if(x.split[j]==" RI")
{
if(type=="MDN35.ALK") RI.MDN35.ALK=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="MDN35.FAME") RI.MDN35.FAME=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="VAR5.ALK") RI.VAR5.ALK=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="VAR5.FAME") RI.VAR5.FAME=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
}
if(x.split[j]==" MST SEL MASS") SelMZ <- as.vector(sapply(strsplit(x.split[j+1], "\\|")[[1]],function(z){
if (grepl('NA',z)) {
return(NA)
} else {
return(as.numeric(z))
}
}))
if(x.split[j]=="CAS#") CAS=x.split[j+1]
if(x.split[j]=="Formula") Formula=x.split[j+1]
if(x.split[j]==" METB InChI") InChi= strsplit(x.split[j+1], "=")[[1]][2]
if(x.split[j]==" METB KEGG") KEGG=x.split[j+1]
if(x.split[j]=="MW")
{
no.dot <- apply(as.matrix(x.split[j+1]), 2, gsub, patt="\\.", replace="")
MW=as.numeric(apply(as.matrix(no.dot), 2, gsub, patt=",", replace="."))
}
if(x.split[j]=="Comment") Comment=x.split[j+1]
if(x.split[j]==" GMD LINK") GMD.LINK=paste(x.split[j+1],":",x.split[j+2],sep="")
if(x.split[j]==" GMD VERS") GMD.VERS= paste(x.split[j+1],":",x.split[j+2],sep="")
}
#cat(Name, "\n")
s.spl <- strsplit(Name," ")[[1]]; Name <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Synon," ")[[1]]; Synon <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(CAS," ")[[1]]; CAS <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Formula," ")[[1]]; Formula <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(KEGG," ")[[1]]; KEGG <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Comment," ")[[1]]; Comment <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(GMD.LINK," ")[[1]]; GMD.LINK <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(GMD.VERS," ")[[1]]; GMD.VERS <- paste(s.spl[-1], collapse=" ")
compound.info <- list(Name=Name, Synon=Synon, RI.VAR5.FAME=RI.VAR5.FAME, RI.VAR5.ALK=RI.VAR5.ALK, RI.MDN35.FAME=RI.MDN35.FAME, RI.MDN35.ALK=RI.MDN35.ALK, SelMZ=SelMZ, CAS=CAS, InChi=InChi, Formula=Formula, MW=MW, KEGG=KEGG, Comment=Comment, GMD.LINK=GMD.LINK, GMD.VERS=GMD.VERS, Spectra=Spectra)
compound.info
}
get.compound.info_MSP <- function(k, Spl.List, type)
{
#kmain <<-k
x <- Spl.List[[k]]
x.split <- unlist(apply(as.matrix(x),1, function(x) {strsplit(x,":")[[1]]}), recursive=T)
Name=" "
Synon=" "
RI.VAR5.FAME=0
RI.VAR5.ALK=0
RI.MDN35.FAME=0
RI.MDN35.ALK=0
CAS=" "
Formula=" "
InChi=" "
KEGG=""
MW=0
Comment=" "
GMD.LINK=" "
GMD.VERS=" "
SelMZ=NA
Spectra <- ""
Caps <- apply(as.matrix(x),1, function(x) {strsplit(x,":")[[1]]})
Sp.Ini <- which(lapply(Caps,function(y)y[1])=="Num Peaks" | lapply(Caps,function(y)y[1])=="Num peaks")
Spectra.semicolon <- paste(x[(Sp.Ini+1):length(x)],collapse="")
Spectra.semicolon <- gsub(' {2,}', ' ', Spectra.semicolon)
if(strsplit(Spectra.semicolon, '')[[1]][1]==' ') Spectra.semicolon <- paste(strsplit(Spectra.semicolon, '')[[1]][-1], collapse='')
if(length(grep(";", Spectra.semicolon))!=0){
Spectra.dot <- sapply(strsplit(Spectra.semicolon, ";")[[1]], function(y) paste(strsplit(y, " ")[[1]], collapse=":"))
}else{
Spectra.dot <- sapply(x[(Sp.Ini+1):length(x)], function(y) paste(strsplit(y, " ")[[1]], collapse=":"))
}
Spectra.dot <- sapply(Spectra.dot, function(y) {
yV <- y
nVs <- strsplit(y[1], '')[[1]] %in% c(0:9)
if(nVs[1]==FALSE) yV <- paste(strsplit(y, '')[[1]][-1], collapse='')
if(nVs[length(nVs)]==FALSE) yV <- paste(strsplit(y, '')[[1]][-length(nVs)], collapse='')
yV
})
Spectra <- paste(Spectra.dot , collapse=" ")
for(j in 1:length(x.split))
{
if(x.split[j]=="Name") Name=x.split[j+1]
#if(x.split[j]==" MST SEL MASS") SelMZ <- as.vector(sapply(strsplit(x.split[j+1], "\\|"), as.numeric))
if(x.split[j]=="CAS#" | x.split[j]=="CASNO") CAS=x.split[j+1]
if(x.split[j]=="Formula") Formula=x.split[j+1]
if(x.split[j]=="DB#") InChi= x.split[j+1]
#if(x.split[j]==" METB KEGG") KEGG=x.split[j+1]
if(x.split[j]=="RI")
{
if(type=="MDN35.ALK") RI.MDN35.ALK=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="MDN35.FAME") RI.MDN35.FAME=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="VAR5.ALK") RI.VAR5.ALK=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
if(type=="VAR5.FAME") RI.VAR5.FAME=as.numeric(apply(as.matrix(x.split[j+1]), 2, gsub, patt=",", replace="."))
}
if(x.split[j]=="MW")
{
no.dot <- apply(as.matrix(x.split[j+1]), 2, gsub, patt="\\.", replace="")
MW=as.numeric(apply(as.matrix(no.dot), 2, gsub, patt=",", replace="."))
}
if(x.split[j]=="Comments" | x.split[j]=="Comment") Comment=x.split[j+1]
#if(x.split[j]==" GMD LINK") GMD.LINK=paste(x.split[j+1],":",x.split[j+2],sep="")
#if(x.split[j]==" GMD VERS") GMD.VERS= paste(x.split[j+1],":",x.split[j+2],sep="")
}
#cat(Name, "\n")
s.spl <- strsplit(Name," ")[[1]]; Name <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Synon," ")[[1]]; Synon <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(CAS," ")[[1]]; CAS <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Formula," ")[[1]]; Formula <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(KEGG," ")[[1]]; KEGG <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(Comment," ")[[1]]; Comment <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(GMD.LINK," ")[[1]]; GMD.LINK <- paste(s.spl[-1], collapse=" ")
s.spl <- strsplit(GMD.VERS," ")[[1]]; GMD.VERS <- paste(s.spl[-1], collapse=" ")
compound.info <- list(Name=Name, Synon=Synon, RI.VAR5.FAME=RI.VAR5.FAME, RI.VAR5.ALK=RI.VAR5.ALK, RI.MDN35.FAME=RI.MDN35.FAME, RI.MDN35.ALK=RI.MDN35.ALK, SelMZ=SelMZ, CAS=CAS, InChi=InChi, Formula=Formula, MW=MW, KEGG=KEGG, Comment=Comment, GMD.LINK=GMD.LINK, GMD.VERS=GMD.VERS, Spectra=Spectra)
compound.info
}
list.DB <- function(DB.object)
{
k <- 1
Cont <- 1
Spl.List <- list()
for(i in 1:length(DB.object))
{
if(DB.object[i]=="")
{
Spl.List[Cont] <- list(Compound=DB.object[k:(i-1)])
k <- i + 1
Cont <- Cont + 1
}
}
Spl.List
}
#' @name importGMD
#' @aliases importGMD
#' @title Import MSP files from GMD to R
#' @description Import the Golm Metabolome Database.
#' @usage importGMD(filename, DB.name, DB.version, DB.info,
#' type = c("VAR5.ALK","VAR5.FAME","MDN35.ALK", "MDN35.FAME"))
#' @param filename The filepath containing the GMD database file.
#' @param DB.name The name of the database (each user may chose its own name
#' @param DB.version The version of the database (each user may chose its own version)
#' @param DB.info Some info about the database for further reference
#' @param type The type of RI to be imported from the database
#' @details For more details, please see the eRah manual
#' @export
importGMD <- function(filename, DB.name, DB.version, DB.info, type=c("VAR5.ALK","VAR5.FAME","MDN35.ALK", "MDN35.FAME"))
{
DB.MSP <- readLines(filename)
Spl.List <- list.DB(DB.MSP)
import.database <- list()
import.database <- lapply(1:length(Spl.List), function(x) get.compound.info_GMD(x, Spl.List, type))
final.database <- new("eRah_DB", name=DB.name, version=DB.version, info=DB.info, database=import.database)
final.database
}
#' @name importMSP
#' @aliases importMSP
#' @title Import MSP files to R
#' @description Import MS libraries in MSP format to eRah DB format.
#' @usage importMSP(filename, DB.name, DB.version, DB.info)
#' @param filename The filepath containing the MSP library file.
#' @param DB.name The name of the database (each user may chose its own name)
#' @param DB.version The version of the database (each user may chose its own version)
#' @param DB.info Some info about the database for further reference
#' @details
#' The MSP input file should look like:
#'
#' -----
#'
#' Name: Metabolite_name
#'
#' Formula: H2O
#'
#' MW: 666
#'
#' ExactMass: 666.266106
#'
#' CAS#: 11-22-3
#'
#' DB#: 1
#'
#' Comments: Metabolite_name reference standard
#'
#' Num Peaks: XX
#'
#' 53 1; 54 2; 55 5; 56 2; 57 2;
#'
#' 58 14; 59 18; 60 1000; 61 2; 67 1;
#'
#' Name: Metabolite_name_2
#'
#' Formula: H2O2
#'
#' MW: 999
#'
#' ExactMass: 999.266106
#'
#' CAS#: 22-33-4
#'
#' DB#: 2
#'
#'Comments: Metabolite_name_"" reference standard
#'
#' Num Peaks: XX
#'
#' 66 10; 67 1000; 155 560; 156 800; 157 2;
#'
#'158 14; 159 1; 160 100; 161 2; 167 1;
#'
#' -------
#'
#' OR
#'
#' -----
#'
#' Name: Metabolite_name
#'
#' Formula: H2O
#'
#' MW: 666
#'
#' ExactMass: 666.266106
#'
#' CASNO: 11-22-3
#'
#' DB#: 1
#'
#' Comment: Metabolite_name reference standard
#'
#' Num peaks: XX
#'
#' 53 1
#'
#' 54 2
#'
#' 55 5
#'
#' Name: Metabolite_name_2
#'
#' Formula: H2O2
#'
#' MW: 999
#'
#' ExactMass: 999.266106
#'
#' CASNO: 22-33-4
#'
#' DB#: 2
#'
#' Comment: Metabolite_name_"" reference standard
#'
#' Num Peaks: XX
#'
#' 66 10
#'
#' 67 1000
#'
#' 155 560
#'
#' -------
#'
#' Or combinations of both.
#'
#'
#' For more details, please see the eRah manual.
#' @export
#' @importFrom methods new
importMSP <- function(filename, DB.name, DB.version, DB.info)
{
DB.MSP <- readLines(filename)
Spl.List <- list.DB(DB.MSP)
import.database <- list()
OutFromList <- unlist(lapply(Spl.List, function(x) all(unlist(x)=="")))
Spl.List <- Spl.List[!OutFromList]
import.database <- lapply(1:length(Spl.List), function(x) get.compound.info_MSP(x, Spl.List, type="VAR5.ALK"))
final.database <- new("eRah_DB", name=DB.name, version=DB.version, info=DB.info, database=import.database)
final.database
}
Try the erah package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.