R/Metlin.annotation.R
In yufree/xMSannotator: xMSannotator: R package for network based annotation of metabolomics data.
Defines functions
Metlin.annotation
Documented in
Metlin.annotation
#' Human Metabolome Database', 'ChEMBL', 'ChEBI', 'NIAID','Pesticide Common
#' Names','SMPDB Small Molecule Pathway Database',
#' MeSH','LipidMAPS','ChemBank','BioCyc')
#'
#' Human Metabolome Database', 'ChEMBL', 'ChEBI', 'NIAID','Pesticide Common
#' Names','SMPDB Small Molecule Pathway Database',
#' MeSH','LipidMAPS','ChemBank','BioCyc')
#'
#'
Metlin.annotation <- function(dataA, max.mz.diff = 10, queryadductlist = c("M+H"),
xMSannotator.outloc, tokenstr = NA) {
data_a <- as.data.frame(dataA)
# print('Using the 1st column as \'mz\' for
# annotation.')
if (is.na(tokenstr) == TRUE) {
stop("Please specify a valid METLIN security token. \nCreate a METLIN account to obtain a token: \n http://metlin.scripps.edu/soap/register.php")
}
mzlist <- data_a[, 1]
# =c('PubChem','MassBank', 'EPA DSSTox','EPA
# Toxcast','NIST Chemistry WebBook','KEGG',
#'Human Metabolome Database', 'ChEMBL', 'ChEBI', 'NIAID','Pesticide Common Names','SMPDB Small Molecule Pathway Database',
#'MeSH','LipidMAPS','ChemBank','BioCyc')
dir.create(xMSannotator.outloc, showWarnings = FALSE)
setwd(xMSannotator.outloc)
adductlist = c(1.00727, 22.989171, 38.963171, -35.012729,
-17.002729, 0.0227, 7.01597, 18.033871, 33.033471,
42.033871, 44.971171, 64.015771, 1.00727, 11.998247,
22.989171, 1.00727, 8.33459, 15.6618, -19.01839,
-1.00727, 18.998371, 20.974671, 34.969371, 36.948571,
44.998171, 59.013871, 78.918885, -1.00727, -1.00727)
alladducts <- c("M+H", "M+Na", "M+K", "M+H-2H2O", "M+H-H2O",
"M-H2O+NH4", "M+Li", "M+NH4", "M+CH3OH+H", "M+ACN+H",
"M+2Na-H", "M+ACN+Na", "M+2H", "M+H+Na", "M+2Na",
"M+3H", "M+2H+Na", "M+2Na+H", "M-H2O-H", "M-H", "M+F",
"M+Na-2H", "M+Cl", "M+K-2H", "M+FA-H", "M+CH3COO",
"M+Br", "M-2H", "M-3H")
names(adductlist) <- c("M+H", "M+Na", "M+K", "M+H-2H2O",
"M+H-H2O", "M-H2O+NH4", "M+Li", "M+NH4", "M+CH3OH+H",
"M+ACN+H", "M+2Na-H", "M+ACN+Na", "M+2H", "M+H+Na",
"M+2Na", "M+3H", "M+2H+Na", "M+2Na+H", "M-H2O-H",
"M-H", "M+F", "M+Na-2H", "M+Cl", "M+K-2H", "M+FA-H",
"M+CH3COO", "M+Br", "M-2H", "M-3H")
mult_charge <- c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
2, 2, 2, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3)
names(mult_charge) <- c("M+H", "M+Na", "M+K", "M+H-2H2O",
"M+H-H2O", "M-H2O+NH4", "M+Li", "M+NH4", "M+CH3OH+H",
"M+ACN+H", "M+2Na-H", "M+ACN+Na", "M+2H", "M+H+Na",
"M+2Na", "M+3H", "M+2H+Na", "M+2Na+H", "M-H2O-H",
"M-H", "M+F", "M+Na-2H", "M+Cl", "M+K-2H", "M+FA-H",
"M+CH3COO", "M+Br", "M-2H", "M-3H")
if (queryadductlist[1] == "positive") {
queryadductlist <- c("M+H", "M+Na", "M+K", "M+H-2H2O",
"M+H-H2O", "M+Li", "M+NH4", "M+CH3OH+H", "M+ACN+H",
"M+2Na-H", "M+ACN+Na", "M+2H", "M+H+Na", "M+2Na",
"M+3H", "M+2H+Na", "M+2Na+H")
} else {
if (queryadductlist[1] == "negative") {
queryadductlist <- c("M-H2O-H", "M-H", "M+F",
"M+Na-2H", "M+Cl", "M+K-2H", "M+FA-H", "M+CH3COO",
"M-2H", "M-3H")
} else {
if (queryadductlist[1] == "all") {
queryadductlist <- alladducts
} else {
if (length(which(queryadductlist %in% alladducts ==
FALSE)) > 0) {
errormsg <- paste("Adduct should be one of:",
sep = "")
for (i in alladducts) {
errormsg <- paste(errormsg, i, sep = " ; ")
}
stop(errormsg, "\n\nUsage: feat.batch.annotation.Metlin(dataA,max.mz.diff=10, queryadductlist=c(\"M+H\", \"M+Na\"), xMSannotator.outloc, numnodes=1)",
"\n\n OR feat.batch.annotation.Metlin(dataA,max.mz.diff=10, queryadductlist=c(\"positive\"), xMSannotator.outloc, numnodes=1)",
"\n\n OR feat.batch.annotation.Metlin(dataA,max.mz.diff=10, queryadductlist=c(\"negative\"), xMSannotator.outloc, numnodes=1)",
"\n\n OR feat.batch.annotation.Metlin(dataA,max.mz.diff=10, queryadductlist=c(\"all\"), xMSannotator.outloc, numnodes=1)")
}
}
}
}
parentres = {
}
res <- {
}
cnames <- c("", "Adduct", "Query.m/z", "MetlinID", "Mass",
"Name", "Molecular.Formula")
for (adnum in 1:length(queryadductlist)) {
adductname = queryadductlist[adnum]
# adductmass=adductlist[as.character(adductname)]
adductname <- gsub(x = adductname, pattern = "\\+",
replacement = "%2B", perl = TRUE)
# tokenstr<-'A30GCsqF5VkBoHlH'
mz_seq <- seq(1, length(mzlist), 500)
temp_res <- {
}
for (mzind in 1:length(mzlist)) {
url <- paste("http://metlin.scripps.edu/REST/search/index.php?token=",
tokenstr, sep = "")
suburl <- {
}
suburl <- paste(suburl, "&mass[]=", mzlist[mzind],
sep = "")
url <- paste(url, suburl, "&adduct[]=", adductname,
"&tolunits=ppm&tolerance=", max.mz.diff,
sep = "")
# print(url)
# 195.0877&mass[]=181.0702&adduct[]=M%2BH&tolunits=ppm&tolerance=30',sep='')
r1 <- getURL(url)
parser <- newJSONParser()
parser$addData(r1)
# metlinres<-parser$getObject()
metlinres <- try(parser$getObject(), silent = TRUE)
# print(length(metlinres))
if (is(metlinres, "try-error")) {
cur_res <- {
}
} else {
for (m1 in 1:length(metlinres)) {
metlin_res_m1 <- metlinres[[m1]]
# print(metlin_res_m1)
for (m2 in 1:length(metlin_res_m1)) {
cur_res <- metlin_res_m1[[m2]]
# print(length(cur_res))
if (length(cur_res) > 1) {
html_link = paste("<a href=http://metlin.scripps.edu/metabo_info.php?molid=",
cur_res$molid, ">", cur_res$molid,
"</a>", sep = "")
temp_res <- rbind(temp_res, c(mzlist[mzind],
html_link, cur_res$molid, cur_res$mass,
cur_res$name, cur_res$formula))
}
}
}
}
}
res <- unique(temp_res)
text_res <- {
}
if (length(res) > 0) {
adductname <- gsub(x = adductname, pattern = "%2B",
replacement = "\\+", perl = TRUE)
adductname = rep(adductname, dim(res)[1])
temp_res <- cbind(adductname, res)
temp_res <- as.matrix(temp_res)
if (dim(temp_res)[2] == 1) {
temp_res <- t(temp_res)
temp_res <- as.data.frame(temp_res)
}
bad_rows <- which(temp_res[, 2] == "1")
if (length(bad_rows) > 0) {
temp_res <- temp_res[-bad_rows, ]
temp_res <- as.matrix(temp_res)
if (dim(temp_res)[2] == 1) {
temp_res <- t(temp_res)
}
}
# temp_res<-as.data.frame(temp_res)
colnames(temp_res) = NULL
text_resindex <- c(1, 2, 4:7)
text_res <- temp_res[, c(text_resindex)]
text_res <- as.matrix(text_res)
text_res <- as.data.frame(text_res)
sernum = seq(1, dim(text_res)[1])
text_res <- cbind(sernum, text_res)
colnames(text_res) = cnames
parentres = rbind(parentres, temp_res)
# rm(temp_res)
colnames(parentres) = NULL
fname = paste(xMSannotator.outloc, "/Metlin_annotation_results_",
queryadductlist[adnum], ".txt", sep = "")
write.table(text_res, file = fname, sep = "\t",
row.names = FALSE)
}
Sys.sleep(2)
}
html_res <- {
}
text_res <- {
}
if (length(parentres) > 0) {
res <- parentres[order(parentres[, 2]), ]
res <- as.matrix(res)
if (dim(res)[2] == 1) {
res <- t(res)
}
html_resindex <- c(1, 2, 3, 5:7)
html_res <- res[, c(html_resindex)]
html_res <- as.matrix(html_res)
if (dim(html_res)[2] == 1) {
html_res <- t(html_res)
}
# sernum=seq(1,dim(html_res)[1])
# html_res<-cbind(sernum,html_res)
html_res <- as.data.frame(html_res)
cnames <- c("Adduct", "Query.m/z", "MetlinID", "Mass",
"Name", "Molecular.Formula")
colnames(html_res) <- cnames
fname = paste("Metlin_annotation_results", sep = "")
unlink(fname)
HTMLInitFile(filename = fname, Title = "Metlin annotation results",
outdir = xMSannotator.outloc)
fname = paste(xMSannotator.outloc, "/Metlin_annotation_results.html",
sep = "")
HTML(html_res, file = fname, Border = 1, innerBorder = 1,
useCSS = TRUE)
HTMLEndFile(file = fname)
text_resindex <- c(1, 2, 4:7)
text_res <- res[, c(text_resindex)]
text_res <- as.matrix(text_res)
text_res <- as.data.frame(text_res)
sernum = seq(1, dim(text_res)[1])
text_res <- cbind(sernum, text_res)
cnames <- c("", "Adduct", "Query.m/z", "MetlinID",
"Mass", "Name", "Molecular.Formula")
colnames(text_res) = cnames
fname = paste(xMSannotator.outloc, "/Metlin_annotation_results_alladducts.txt",
sep = "")
write.table(text_res, file = fname, sep = "\t", row.names = FALSE)
}
return(list(text.res = text_res, html.res = html_res))
}
yufree/xMSannotator documentation built on Oct. 31, 2022, 12:20 a.m.
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Defines functions Metlin.annotation
Documented in Metlin.annotation
#' Human Metabolome Database', 'ChEMBL', 'ChEBI', 'NIAID','Pesticide Common
#' Names','SMPDB Small Molecule Pathway Database',
#' MeSH','LipidMAPS','ChemBank','BioCyc')
#'
#' Human Metabolome Database', 'ChEMBL', 'ChEBI', 'NIAID','Pesticide Common
#' Names','SMPDB Small Molecule Pathway Database',
#' MeSH','LipidMAPS','ChemBank','BioCyc')
#'
#'
Metlin.annotation <- function(dataA, max.mz.diff = 10, queryadductlist = c("M+H"),
xMSannotator.outloc, tokenstr = NA) {
data_a <- as.data.frame(dataA)
# print('Using the 1st column as \'mz\' for
# annotation.')
if (is.na(tokenstr) == TRUE) {
stop("Please specify a valid METLIN security token. \nCreate a METLIN account to obtain a token: \n http://metlin.scripps.edu/soap/register.php")
}
mzlist <- data_a[, 1]
# =c('PubChem','MassBank', 'EPA DSSTox','EPA
# Toxcast','NIST Chemistry WebBook','KEGG',
#'Human Metabolome Database', 'ChEMBL', 'ChEBI', 'NIAID','Pesticide Common Names','SMPDB Small Molecule Pathway Database',
#'MeSH','LipidMAPS','ChemBank','BioCyc')
dir.create(xMSannotator.outloc, showWarnings = FALSE)
setwd(xMSannotator.outloc)
adductlist = c(1.00727, 22.989171, 38.963171, -35.012729,
-17.002729, 0.0227, 7.01597, 18.033871, 33.033471,
42.033871, 44.971171, 64.015771, 1.00727, 11.998247,
22.989171, 1.00727, 8.33459, 15.6618, -19.01839,
-1.00727, 18.998371, 20.974671, 34.969371, 36.948571,
44.998171, 59.013871, 78.918885, -1.00727, -1.00727)
alladducts <- c("M+H", "M+Na", "M+K", "M+H-2H2O", "M+H-H2O",
"M-H2O+NH4", "M+Li", "M+NH4", "M+CH3OH+H", "M+ACN+H",
"M+2Na-H", "M+ACN+Na", "M+2H", "M+H+Na", "M+2Na",
"M+3H", "M+2H+Na", "M+2Na+H", "M-H2O-H", "M-H", "M+F",
"M+Na-2H", "M+Cl", "M+K-2H", "M+FA-H", "M+CH3COO",
"M+Br", "M-2H", "M-3H")
names(adductlist) <- c("M+H", "M+Na", "M+K", "M+H-2H2O",
"M+H-H2O", "M-H2O+NH4", "M+Li", "M+NH4", "M+CH3OH+H",
"M+ACN+H", "M+2Na-H", "M+ACN+Na", "M+2H", "M+H+Na",
"M+2Na", "M+3H", "M+2H+Na", "M+2Na+H", "M-H2O-H",
"M-H", "M+F", "M+Na-2H", "M+Cl", "M+K-2H", "M+FA-H",
"M+CH3COO", "M+Br", "M-2H", "M-3H")
mult_charge <- c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
2, 2, 2, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3)
names(mult_charge) <- c("M+H", "M+Na", "M+K", "M+H-2H2O",
"M+H-H2O", "M-H2O+NH4", "M+Li", "M+NH4", "M+CH3OH+H",
"M+ACN+H", "M+2Na-H", "M+ACN+Na", "M+2H", "M+H+Na",
"M+2Na", "M+3H", "M+2H+Na", "M+2Na+H", "M-H2O-H",
"M-H", "M+F", "M+Na-2H", "M+Cl", "M+K-2H", "M+FA-H",
"M+CH3COO", "M+Br", "M-2H", "M-3H")
if (queryadductlist[1] == "positive") {
queryadductlist <- c("M+H", "M+Na", "M+K", "M+H-2H2O",
"M+H-H2O", "M+Li", "M+NH4", "M+CH3OH+H", "M+ACN+H",
"M+2Na-H", "M+ACN+Na", "M+2H", "M+H+Na", "M+2Na",
"M+3H", "M+2H+Na", "M+2Na+H")
} else {
if (queryadductlist[1] == "negative") {
queryadductlist <- c("M-H2O-H", "M-H", "M+F",
"M+Na-2H", "M+Cl", "M+K-2H", "M+FA-H", "M+CH3COO",
"M-2H", "M-3H")
} else {
if (queryadductlist[1] == "all") {
queryadductlist <- alladducts
} else {
if (length(which(queryadductlist %in% alladducts ==
FALSE)) > 0) {
errormsg <- paste("Adduct should be one of:",
sep = "")
for (i in alladducts) {
errormsg <- paste(errormsg, i, sep = " ; ")
}
stop(errormsg, "\n\nUsage: feat.batch.annotation.Metlin(dataA,max.mz.diff=10, queryadductlist=c(\"M+H\", \"M+Na\"), xMSannotator.outloc, numnodes=1)",
"\n\n OR feat.batch.annotation.Metlin(dataA,max.mz.diff=10, queryadductlist=c(\"positive\"), xMSannotator.outloc, numnodes=1)",
"\n\n OR feat.batch.annotation.Metlin(dataA,max.mz.diff=10, queryadductlist=c(\"negative\"), xMSannotator.outloc, numnodes=1)",
"\n\n OR feat.batch.annotation.Metlin(dataA,max.mz.diff=10, queryadductlist=c(\"all\"), xMSannotator.outloc, numnodes=1)")
}
}
}
}
parentres = {
}
res <- {
}
cnames <- c("", "Adduct", "Query.m/z", "MetlinID", "Mass",
"Name", "Molecular.Formula")
for (adnum in 1:length(queryadductlist)) {
adductname = queryadductlist[adnum]
# adductmass=adductlist[as.character(adductname)]
adductname <- gsub(x = adductname, pattern = "\\+",
replacement = "%2B", perl = TRUE)
# tokenstr<-'A30GCsqF5VkBoHlH'
mz_seq <- seq(1, length(mzlist), 500)
temp_res <- {
}
for (mzind in 1:length(mzlist)) {
url <- paste("http://metlin.scripps.edu/REST/search/index.php?token=",
tokenstr, sep = "")
suburl <- {
}
suburl <- paste(suburl, "&mass[]=", mzlist[mzind],
sep = "")
url <- paste(url, suburl, "&adduct[]=", adductname,
"&tolunits=ppm&tolerance=", max.mz.diff,
sep = "")
# print(url)
# 195.0877&mass[]=181.0702&adduct[]=M%2BH&tolunits=ppm&tolerance=30',sep='')
r1 <- getURL(url)
parser <- newJSONParser()
parser$addData(r1)
# metlinres<-parser$getObject()
metlinres <- try(parser$getObject(), silent = TRUE)
# print(length(metlinres))
if (is(metlinres, "try-error")) {
cur_res <- {
}
} else {
for (m1 in 1:length(metlinres)) {
metlin_res_m1 <- metlinres[[m1]]
# print(metlin_res_m1)
for (m2 in 1:length(metlin_res_m1)) {
cur_res <- metlin_res_m1[[m2]]
# print(length(cur_res))
if (length(cur_res) > 1) {
html_link = paste("<a href=http://metlin.scripps.edu/metabo_info.php?molid=",
cur_res$molid, ">", cur_res$molid,
"</a>", sep = "")
temp_res <- rbind(temp_res, c(mzlist[mzind],
html_link, cur_res$molid, cur_res$mass,
cur_res$name, cur_res$formula))
}
}
}
}
}
res <- unique(temp_res)
text_res <- {
}
if (length(res) > 0) {
adductname <- gsub(x = adductname, pattern = "%2B",
replacement = "\\+", perl = TRUE)
adductname = rep(adductname, dim(res)[1])
temp_res <- cbind(adductname, res)
temp_res <- as.matrix(temp_res)
if (dim(temp_res)[2] == 1) {
temp_res <- t(temp_res)
temp_res <- as.data.frame(temp_res)
}
bad_rows <- which(temp_res[, 2] == "1")
if (length(bad_rows) > 0) {
temp_res <- temp_res[-bad_rows, ]
temp_res <- as.matrix(temp_res)
if (dim(temp_res)[2] == 1) {
temp_res <- t(temp_res)
}
}
# temp_res<-as.data.frame(temp_res)
colnames(temp_res) = NULL
text_resindex <- c(1, 2, 4:7)
text_res <- temp_res[, c(text_resindex)]
text_res <- as.matrix(text_res)
text_res <- as.data.frame(text_res)
sernum = seq(1, dim(text_res)[1])
text_res <- cbind(sernum, text_res)
colnames(text_res) = cnames
parentres = rbind(parentres, temp_res)
# rm(temp_res)
colnames(parentres) = NULL
fname = paste(xMSannotator.outloc, "/Metlin_annotation_results_",
queryadductlist[adnum], ".txt", sep = "")
write.table(text_res, file = fname, sep = "\t",
row.names = FALSE)
}
Sys.sleep(2)
}
html_res <- {
}
text_res <- {
}
if (length(parentres) > 0) {
res <- parentres[order(parentres[, 2]), ]
res <- as.matrix(res)
if (dim(res)[2] == 1) {
res <- t(res)
}
html_resindex <- c(1, 2, 3, 5:7)
html_res <- res[, c(html_resindex)]
html_res <- as.matrix(html_res)
if (dim(html_res)[2] == 1) {
html_res <- t(html_res)
}
# sernum=seq(1,dim(html_res)[1])
# html_res<-cbind(sernum,html_res)
html_res <- as.data.frame(html_res)
cnames <- c("Adduct", "Query.m/z", "MetlinID", "Mass",
"Name", "Molecular.Formula")
colnames(html_res) <- cnames
fname = paste("Metlin_annotation_results", sep = "")
unlink(fname)
HTMLInitFile(filename = fname, Title = "Metlin annotation results",
outdir = xMSannotator.outloc)
fname = paste(xMSannotator.outloc, "/Metlin_annotation_results.html",
sep = "")
HTML(html_res, file = fname, Border = 1, innerBorder = 1,
useCSS = TRUE)
HTMLEndFile(file = fname)
text_resindex <- c(1, 2, 4:7)
text_res <- res[, c(text_resindex)]
text_res <- as.matrix(text_res)
text_res <- as.data.frame(text_res)
sernum = seq(1, dim(text_res)[1])
text_res <- cbind(sernum, text_res)
cnames <- c("", "Adduct", "Query.m/z", "MetlinID",
"Mass", "Name", "Molecular.Formula")
colnames(text_res) = cnames
fname = paste(xMSannotator.outloc, "/Metlin_annotation_results_alladducts.txt",
sep = "")
write.table(text_res, file = fname, sep = "\t", row.names = FALSE)
}
return(list(text.res = text_res, html.res = html_res))
}
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