/
read_write_msp.R
807 lines (682 loc) · 24.9 KB
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read_write_msp.R
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#---------------------------------------------------------------------------
#' @title read_msp
#' @description Read MSP data.
#' \lifecycle{experimental}
#' @author Xiaotao Shen
#' \email{shenxt1990@@163.com}
#' @param file The vector of names of ms2 files. MS2 file must be msp format.
#' @param threads threads number.
#' @return Return ms2 data. This is a list.
#' @export
read_msp = function(file,
threads = 3) {
cat(crayon::green("Reading msp data...\n"))
# future::plan(strategy = future::multisession, workers = threads)
msp.data <- readLines(file)
if (length(grep("BEGIN IONS", msp.data)) > 0) {
msp.data <- msp.data[msp.data != ""]
temp.idx1 <- grep("BEGIN IONS", msp.data)
temp.idx2 <- grep("END IONS", msp.data)
if (length(temp.idx2) < length(temp.idx1)) {
temp.idx2 <- c(temp.idx2, length(msp.data))
}
temp.idx <-
purrr::map2(.x = temp.idx1, temp.idx2, function(x, y) {
c(x + 1, y - 1)
})
ms2_spec <- purrr::map(
.x = temp.idx,
.f = function(x) {
temp_spec <- msp.data[x[1]:x[2]]
temp_spec <- temp_spec
spec_info <-
temp_spec[stringr::str_detect(temp_spec, "[A-Za-z]")]
spec <-
temp_spec[!stringr::str_detect(temp_spec, "[A-Za-z]")]
spec_info <- stringr::str_split(spec_info, "\\=") %>%
do.call(rbind, .)
mz <-
as.numeric(spec_info[grep("MASS|MZ", spec_info[, 1]), 2])
rt <-
as.numeric(spec_info[grep("RT|RETETION", spec_info[, 1]), 2])
spec_info <- c(mz = mz, rt = rt)
spec <- purrr::map(
.x = spec,
.f = function(x) {
stringr::str_split(x, " ")[[1]] %>% as.numeric()
}
) %>%
do.call(rbind, .)
spec <-
spec %>% as.matrix()
colnames(spec) <- c("mz", "intensity")
spec <- list(info = spec_info, spec = spec)
spec
}
)
return(ms2_spec)
} else{
# n.tot <- length(msp.data)
n.null <- which(msp.data == '')
temp.idx1 <- c(1, n.null[-length(n.null)])
temp.idx2 <- n.null - 1
temp.idx <- data.frame(temp.idx1, temp.idx2,
stringsAsFactors = FALSE)
temp.idx <- apply(temp.idx, 1, list)
temp.idx <- lapply(temp.idx, unlist)
# n.spec <- which(grepl('^\\d', msp.data))
# n.info <- seq(n.tot)[-c(n.spec, n.null)]
pbapply::pboptions(style = 1)
info.spec <- pbapply::pblapply(temp.idx, function(idx) {
temp.msp.data <- msp.data[idx[1]:idx[2]]
temp.msp.data <- temp.msp.data[temp.msp.data != ""]
info.idx <- grep("[A-Za-z]", temp.msp.data)
temp.info <- temp.msp.data[info.idx]
temp.info <- strsplit(temp.info, split = ":")
temp.info <- do.call(rbind, temp.info)
temp.info <- data.frame(temp.info,
stringsAsFactors = FALSE)
temp.info[, 2] <- stringr::str_trim(temp.info[, 2])
colnames(temp.info) <- rownames(temp.info) <- NULL
rownames(temp.info) <- temp.info[, 1]
temp.info <- temp.info[, -1, drop = FALSE]
temp.spec <- temp.msp.data[-info.idx]
if (length(temp.spec) != 0) {
if (length(grep(" ", temp.spec[1])) == 1) {
temp.spec <- strsplit(temp.spec, split = ' ')
}
if (length(grep("\t", temp.spec[1])) == 1) {
temp.spec <- strsplit(x = temp.spec, split = "\t")
}
temp.spec <- do.call(rbind, temp.spec)
temp.spec <- data.frame(temp.spec,
stringsAsFactors = FALSE)
colnames(temp.spec) <- c('mz', 'intensity')
rownames(temp.spec) <- NULL
temp.spec$mz <- as.numeric(as.character(temp.spec$mz))
temp.spec$intensity <- as.numeric(temp.spec$intensity)
temp.spec <- temp.spec[temp.spec$intensity != 0,]
} else{
temp.spec <- NULL
}
list('info' = temp.info,
'spec' = temp.spec)
})
mz.idx <- grep("[Mm][Zz]", rownames(info.spec[[1]][[1]]))
rt.idx <-
grep("Time$|TIME$|time$|^RT|^rt|^Rt", rownames(info.spec[[1]][[1]]))
##fix bug in msp data from metAnalyzer
if (length(rt.idx) == 0) {
cat(crayon::yellow("The msp data are from MetAnalyzer software.\n"))
rt.idx <-
grep("NAME|Name|name", rownames(info.spec[[1]][[1]]))
##rt.idx is the name of peak
info.spec <- lapply(info.spec, function(x) {
info <- x[[1]]
mz <- as.numeric(info[mz.idx, 1])
rt <- as.character(info[rt.idx, 1])
info <- c(mz, rt)
names(info) <- c("mz", "rt")
x[[1]] <- info
x
})
} else{
info.spec <- lapply(info.spec, function(x) {
info <- x[[1]]
mz <- as.numeric(info[mz.idx, 1])
rt <- as.numeric(info[rt.idx, 1])
info <- c(mz, rt)
names(info) <- c("mz", "rt")
x[[1]] <- info
x
})
}
}
remove.idx <-
which(unlist(lapply(info.spec, function(x)
is.null(x[[2]]))))
if (length(remove.idx) > 0) {
info.spec <- info.spec[-remove.idx]
}
info.spec <- info.spec
}
#---------------------------------------------------------------------------
#' @title read_msp_database
#' @description Read MSP data for database.
#' \lifecycle{experimental}
#' @author Xiaotao Shen
#' \email{shenxt1990@@163.com}
#' @param file The vector of names of ms2 files. MS2 file must be msp format.
#' @param threads threads
#' @return Return ms2 data. This is a list.
#' @export
read_msp_database = function(file,
threads = 4) {
msp.data <- readr::read_lines(file)
if (length(grep("BEGIN IONS", msp.data)) > 0) {
msp.data <- msp.data[msp.data != ""]
temp.idx1 <- grep("BEGIN IONS", msp.data)
temp.idx2 <- grep("END IONS", msp.data)
if (length(temp.idx2) < length(temp.idx1)) {
temp.idx2 <- c(temp.idx2, length(msp.data))
}
temp.idx <-
purrr::map2(.x = temp.idx1, temp.idx2, function(x, y) {
c(x + 1, y - 1)
})
# future::plan(strategy = future::multisession, workers = threads)
ms2_spec <- purrr::map(
.x = temp.idx,
.f = function(x) {
temp_spec <- msp.data[x[1]:x[2]]
temp_spec <- temp_spec
spec_info <-
temp_spec[stringr::str_detect(temp_spec, "[A-Za-z]")]
spec <-
temp_spec[!stringr::str_detect(temp_spec, "[A-Za-z]")]
spec_info <- stringr::str_split(spec_info, "\\=") %>%
do.call(rbind, .)
mz <-
as.numeric(spec_info[grep("MASS|MZ", spec_info[, 1]), 2])
rt <-
as.numeric(spec_info[grep("RT|RETETION", spec_info[, 1]), 2])
spec_info <- c(mz = mz, rt = rt)
spec <- purrr::map(
.x = spec,
.f = function(x) {
stringr::str_split(x, " ")[[1]] %>% as.numeric()
}
) %>%
do.call(rbind, .)
spec <-
spec %>% as.matrix()
colnames(spec) <- c("mz", "intensity")
spec <- list(info = spec_info, spec = spec)
spec
}
)
return(ms2_spec)
} else{
# n.tot <- length(msp.data)
n.null <- which(msp.data == '')
temp.idx1 <- c(1, n.null[-length(n.null)])
temp.idx2 <- n.null - 1
temp.idx <- data.frame(temp.idx1, temp.idx2,
stringsAsFactors = FALSE)
temp.idx <- apply(temp.idx, 1, list)
temp.idx <- lapply(temp.idx, unlist)
# n.spec <- which(grepl('^\\d', msp.data))
# n.info <- seq(n.tot)[-c(n.spec, n.null)]
# pbapply::pboptions(style = 1)
info.spec =
purrr::map(
temp.idx,
.f =
function(idx) {
temp.msp.data <- msp.data[idx[1]:idx[2]]
temp.msp.data <-
temp.msp.data[temp.msp.data != ""]
info.idx <-
grep("[A-Za-z]", temp.msp.data)
temp.info <- temp.msp.data[info.idx]
temp.info <-
strsplit(temp.info, split = ":")
temp.info <- do.call(rbind, temp.info)
temp.info <- data.frame(temp.info,
stringsAsFactors = FALSE)
temp.info[, 2] <-
stringr::str_trim(temp.info[, 2])
colnames(temp.info) <-
rownames(temp.info) <- NULL
rownames(temp.info) <- temp.info[, 1]
temp.info <- temp.info[, -1, drop = FALSE]
temp.spec <- temp.msp.data[-info.idx]
if (length(temp.spec) != 0) {
if (length(grep(" ", temp.spec[1])) == 1) {
temp.spec <- strsplit(temp.spec, split = ' ')
}
if (length(grep("\t", temp.spec[1])) == 1) {
temp.spec <- strsplit(x = temp.spec, split = "\t")
}
temp.spec <- do.call(rbind, temp.spec)
temp.spec <- data.frame(temp.spec,
stringsAsFactors = FALSE)
colnames(temp.spec) <-
c('mz', 'intensity')
rownames(temp.spec) <- NULL
temp.spec$mz <-
as.numeric(as.character(temp.spec$mz))
temp.spec$intensity <-
as.numeric(temp.spec$intensity)
temp.spec <-
temp.spec[temp.spec$intensity != 0,]
} else{
temp.spec <- NULL
}
list('info' = temp.info,
'spec' = temp.spec)
}
)
mz.idx <- grep("[Mm][Zz]", rownames(info.spec[[1]][[1]]))
rt.idx <-
grep("Time$|TIME$|time$|^RT|^rt|^Rt", rownames(info.spec[[1]][[1]]))
##fix bug in msp data from metAnalyzer
if (length(rt.idx) == 0) {
cat(crayon::yellow("The msp data are from MetAnalyzer software.\n"))
rt.idx <-
grep("NAME|Name|name", rownames(info.spec[[1]][[1]]))
##rt.idx is the name of peak
info.spec <- lapply(info.spec, function(x) {
info <- x[[1]]
mz <- as.numeric(info[mz.idx, 1])
rt <- as.character(info[rt.idx, 1])
info <- c(mz, rt)
names(info) <- c("mz", "rt")
x[[1]] <- info
x
})
} else{
info.spec <- purrr::map(info.spec, function(x) {
info <- x[[1]]
mz <- as.numeric(info[mz.idx, 1])
rt <- as.numeric(info[rt.idx, 1])
info2 = info[-c(mz.idx, rt.idx), , drop = FALSE]
info1 <- c(mz, rt)
info = c(info1, info2[, 1])
names(info) <- c("mz", "rt", rownames(info2))
x[[1]] <- info
x
})
}
}
remove.idx <-
which(unlist(lapply(info.spec, function(x)
is.null(x[[2]]))))
if (length(remove.idx) > 0) {
info.spec <- info.spec[-remove.idx]
}
info.spec <- info.spec
}
#' ---------------------------------------------------------------------------
#' @title readMSP_MoNA
#' @description Read MSP data from MoNA.
#' \lifecycle{experimental}
#' @author Xiaotao Shen
#' \email{shenxt1990@@163.com}
#' @param file The vector of names of ms2 files. MS2 file must be msp. The msp data must from MoNA.
#' @return Return ms2 data. This is a list.
#' @export
readMSP_MoNA = function(file) {
cat(crayon::yellow("`readMSP_MoNA()` is deprecated, use `read_msp_mona()`.\n"))
cat(crayon::green("Reading MSP data...\n"))
msp.data <- readr::read_lines(file)
n.null <- which(msp.data == '')
temp.idx1 <- c(1, n.null[-length(n.null)])
temp.idx2 <- n.null - 1
temp.idx <- data.frame(temp.idx1, temp.idx2,
stringsAsFactors = FALSE)
rm(list = c("temp.idx1", "temp.idx2"))
gc(verbose = FALSE)
temp.idx <- apply(temp.idx, 1, list)
temp.idx <- lapply(temp.idx, unlist)
temp.idx <- temp.idx[which(unlist(lapply(temp.idx, function(x) {
x[1] != x[2]
})))]
pbapply::pboptions(style = 1)
# fix bug
# for(idx in 1:length(temp.idx)){
# cat(idx, " ")
# idx <- temp.idx[[idx]]
cat(crayon::yellow("Transforming...\n"))
info.spec <- pbapply::pblapply(temp.idx, function(idx) {
if (idx[1] == idx[2])
return(NULL)
temp.msp.data <- msp.data[idx[1]:idx[2]]
temp.msp.data <- temp.msp.data[temp.msp.data != ""]
info.idx <- grep("[A-Za-z]", temp.msp.data)
temp.info <- temp.msp.data[info.idx]
temp.info <-
stringr::str_split(string = temp.info,
pattern = ":",
n = 2)
temp.info <- do.call(rbind, temp.info)
temp.info <- data.frame(temp.info,
stringsAsFactors = FALSE)
temp.info[, 2] <-
stringr::str_trim(temp.info[, 2], side = "both")
temp.info[, 1] <-
stringr::str_trim(temp.info[, 1], side = "both")
colnames(temp.info) <- rownames(temp.info) <- NULL
#combine synons
if (length(grep("Synon", temp.info[, 1])) > 1) {
Synon <-
stringr::str_c(temp.info[stringr::str_which(string = temp.info[, 1], pattern = "Synon"), 2,
drop = TRUE], collapse = ";")
temp.info[which(temp.info[, 1] == "Synon")[1], 2] <- Synon
temp.info <- temp.info[!duplicated(temp.info[, 1]),]
}
rownames(temp.info) <- temp.info[, 1]
temp.info <- temp.info[, -1, drop = FALSE]
temp.spec <- temp.msp.data[-info.idx]
if (length(temp.spec) != 0) {
if (length(grep(" ", temp.spec[1])) == 1) {
temp.spec <- strsplit(temp.spec, split = ' ')
}
if (length(grep("\t", temp.spec[1])) == 1) {
temp.spec <- strsplit(x = temp.spec, split = "\t")
}
temp.spec <- do.call(rbind, temp.spec)
temp.spec <- data.frame(temp.spec,
stringsAsFactors = FALSE)
colnames(temp.spec) <- c('mz', 'intensity')
rownames(temp.spec) <- NULL
temp.spec$mz <- as.numeric(as.character(temp.spec$mz))
temp.spec$intensity <- as.numeric(temp.spec$intensity)
temp.spec <- temp.spec[temp.spec$intensity != 0,]
} else{
temp.spec <- NULL
}
list('info' = temp.info,
'spec' = temp.spec)
})
rm(list = c("msp.data", "temp.idx"))
gc()
##remove NULL
info.spec <- info.spec[!unlist(lapply(info.spec, is.null))]
remove.idx <-
which(unlist(lapply(info.spec, function(x)
is.null(x[[2]]))))
if (length(remove.idx) > 0) {
info.spec <- info.spec[-remove.idx]
}
rm(list = c("remove.idx"))
gc()
info.spec <- info.spec
}
#' ---------------------------------------------------------------------------
#' @title read_msp_mona
#' @description Read MSP data from MoNA.
#' \lifecycle{experimental}
#' @author Xiaotao Shen
#' \email{shenxt1990@@163.com}
#' @param file The vector of names of ms2 files. MS2 file must be msp. The msp data must from MoNA.
#' @param threads The number of threads
#' @return Return ms2 data. This is a list.
#' @export
# sxtTools::setwd_project()
# setwd("other_files/all_ms2_database/mona/2021_6_10/")
# x = read_msp_mona(file = "MoNA-export-LC-MS-MS_Spectra.msp")
read_msp_mona = function(file,
threads = 3) {
cat(crayon::green("Reading msp data from MoNA...\n"))
future::plan(strategy = future::multisession, workers = threads)
ms2 <- furrr::future_map(
.x = file,
.f = function(temp.msp.data) {
msp.data <- readr::read_lines(temp.msp.data, progress = FALSE)
if(tail(msp.data, 1) == ""){
msp.data = msp.data[-length(msp.data)]
}
msp.data[msp.data == ""] = rep(c("END IONS", "BEGIN IONS"), sum(msp.data == "") /
2)
msp.data = c("BEGIN IONS", msp.data, "END IONS")
begin_idx = which(msp.data == "BEGIN IONS")
end_idx = which(msp.data == "END IONS")
msp.data =
purrr::map2(
.x = begin_idx,
.y = end_idx,
.f = function(idx1, idx2) {
temp = msp.data[c(idx1:idx2)]
temp = temp[temp != "BEGIN IONS"]
temp = temp[temp != "END IONS"]
if (length(temp) == 0) {
return(NULL)
}
info = temp[grep(":", temp, value = FALSE)]
info = stringr::str_split(info, ":", n = 2) %>%
do.call(rbind, .) %>%
as.data.frame() %>%
dplyr::rename(info = V1, value = V2)
spec = temp[-grep(":", temp, value = FALSE)]
spec = stringr::str_split(spec, " ") %>%
do.call(rbind, .) %>%
as.data.frame() %>%
dplyr::rename(mz = V1, intensity = V2) %>%
dplyr::mutate(mz = as.numeric(mz),
intensity = as.numeric(intensity)) %>%
as.data.frame()
list(info = info, spec = spec)
}
)
}, .progress = TRUE
)
ms2 = Reduce(`c`, ms2)
cat(crayon::green("Done.\n"))
ms2
}
#' ---------------------------------------------------------------------------
#' @title read_msp_gnps
#' @description Read MSP data from MoNA.
#' \lifecycle{experimental}
#' @author Xiaotao Shen
#' \email{shenxt1990@@163.com}
#' @param file The vector of names of ms2 files. MS2 file must be msp. The msp data must from MoNA.
#' @param threads The number of threads
#' @return Return ms2 data. This is a list.
#' @export
# sxtTools::setwd_project()
# setwd("other_files/all_ms2_database/mona/2021_6_10/")
# x = read_msp_mona(file = "MoNA-export-LC-MS-MS_Spectra.msp")
read_msp_gnps = function(file,
threads = 5) {
pbapply::pboptions(style = 1)
cat(crayon::green("Reading msp data from GNPS...\n"))
future::plan(strategy = future::multisession, workers = threads)
ms2 <- furrr::future_map(
.x = file,
.f = function(temp.msp.data) {
msp.data <- readr::read_lines(temp.msp.data)
msp.data[msp.data == ""] = rep(c("END IONS", "BEGIN IONS"), sum(msp.data == "") /
2)
msp.data = c("BEGIN IONS", msp.data, "END IONS")
begin_idx = which(msp.data == "BEGIN IONS")
end_idx = which(msp.data == "END IONS")
msp.data =
purrr::map2(
.x = begin_idx,
.y = end_idx,
.f = function(idx1, idx2) {
# cat(paste(idx1, idx2, sep = " "))
temp = msp.data[c(idx1:idx2)]
temp = temp[temp != "BEGIN IONS"]
temp = temp[temp != "END IONS"]
if (length(temp) == 0) {
return(NULL)
}
info = temp[grep(":", temp, value = FALSE)]
info = stringr::str_split(info, ":", n = 2) %>%
do.call(rbind, .) %>%
as.data.frame() %>%
dplyr::rename(info = V1, value = V2)
spec = temp[-grep(":", temp, value = FALSE)]
spec = stringr::str_split(spec, "\t") %>%
do.call(rbind, .) %>%
as.data.frame() %>%
dplyr::rename(mz = V1, intensity = V2) %>%
dplyr::mutate(mz = as.numeric(mz),
intensity = as.numeric(intensity)) %>%
as.data.frame()
list(info = info, spec = spec)
}
)
}, .progress = TRUE
)
ms2 = Reduce(`c`, ms2)
cat(crayon::green("Done.\n"))
ms2
}
WriteMSP = function(info, fn.pre, spec.all) {
fn.save <- paste0(fn.pre, '_spectra.msp')
#
sink(fn.save)
for (idx in seq(nrow(info))) {
if (!is.null(spec.all[[idx]])) {
if (nrow(spec.all[[idx]]) > 0) {
mz <- info[idx, 'Mass']
spec <- spec.all[[idx]]
cat('IDX: ', idx, '\n', sep = '')
cat('PRECURSORMZ: ', mz, '\n', sep = '')
cat('Num Peaks: ', nrow(spec), '\n', sep = '')
for (nr in seq(nrow(spec))) {
cat(paste(spec[nr, ], collapse = ' '), '\n', sep = '')
}
cat('\n')
}
}
}
sink()
}
#---------------------------------------------------------------------------
#' @title readMSP
#' @description Read MSP data.
#' \lifecycle{experimental}
#' @author Xiaotao Shen
#' \email{shenxt1990@@163.com}
#' @param file The vector of names of ms2 files. MS2 file must be msp format.
#' @param silence.deprecated Silenc the deprecated information or not.
#' @return Return ms2 data. This is a list.
#' @export
readMSP = function(file,
silence.deprecated = TRUE) {
if (!silence.deprecated) {
cat(crayon::yellow("`readMSP()` is deprecated, use `read_msp()`.\n"))
}
msp.data <- readLines(file)
if (length(grep("BEGIN IONS", msp.data)) > 0) {
msp.data <- msp.data[msp.data != ""]
temp.idx1 <- grep("BEGIN IONS", msp.data)
temp.idx2 <- grep("END IONS", msp.data)
if (length(temp.idx2) < length(temp.idx1)) {
temp.idx2 <- c(temp.idx2, length(msp.data))
}
temp.idx <-
purrr::map2(.x = temp.idx1, temp.idx2, function(x, y) {
c(x + 1, y - 1)
})
ms2_spec <- purrr::map(
.x = temp.idx,
.f = function(x) {
temp_spec <- msp.data[x[1]:x[2]]
temp_spec <- temp_spec
spec_info <-
temp_spec[stringr::str_detect(temp_spec, "[A-Za-z]")]
spec <-
temp_spec[!stringr::str_detect(temp_spec, "[A-Za-z]")]
spec_info <- stringr::str_split(spec_info, "\\=") %>%
do.call(rbind, .)
mz <-
as.numeric(spec_info[grep("MASS|MZ", spec_info[, 1]), 2])
rt <-
as.numeric(spec_info[grep("RT|RETETION", spec_info[, 1]), 2])
spec_info <- c(mz = mz, rt = rt)
spec <- purrr::map(
.x = spec,
.f = function(x) {
stringr::str_split(x, " ")[[1]] %>% as.numeric()
}
) %>%
do.call(rbind, .)
spec <-
spec %>% as.matrix()
colnames(spec) <- c("mz", "intensity")
spec <- list(info = spec_info, spec = spec)
spec
}
)
return(ms2_spec)
} else{
# n.tot <- length(msp.data)
n.null <- which(msp.data == '')
temp.idx1 <- c(1, n.null[-length(n.null)])
temp.idx2 <- n.null - 1
temp.idx <- data.frame(temp.idx1, temp.idx2,
stringsAsFactors = FALSE)
temp.idx <- apply(temp.idx, 1, list)
temp.idx <- lapply(temp.idx, unlist)
# n.spec <- which(grepl('^\\d', msp.data))
# n.info <- seq(n.tot)[-c(n.spec, n.null)]
pbapply::pboptions(style = 1)
info.spec <- pbapply::pblapply(temp.idx, function(idx) {
temp.msp.data <- msp.data[idx[1]:idx[2]]
temp.msp.data <- temp.msp.data[temp.msp.data != ""]
info.idx <- grep("[A-Za-z]", temp.msp.data)
temp.info <- temp.msp.data[info.idx]
temp.info <- strsplit(temp.info, split = ":")
temp.info <- do.call(rbind, temp.info)
temp.info <- data.frame(temp.info,
stringsAsFactors = FALSE)
temp.info[, 2] <- stringr::str_trim(temp.info[, 2])
colnames(temp.info) <- rownames(temp.info) <- NULL
rownames(temp.info) <- temp.info[, 1]
temp.info <- temp.info[, -1, drop = FALSE]
temp.spec <- temp.msp.data[-info.idx]
if (length(temp.spec) != 0) {
if (length(grep(" ", temp.spec[1])) == 1) {
temp.spec <- strsplit(temp.spec, split = ' ')
}
if (length(grep("\t", temp.spec[1])) == 1) {
temp.spec <- strsplit(x = temp.spec, split = "\t")
}
temp.spec <- do.call(rbind, temp.spec)
temp.spec <- data.frame(temp.spec,
stringsAsFactors = FALSE)
colnames(temp.spec) <- c('mz', 'intensity')
rownames(temp.spec) <- NULL
temp.spec$mz <- as.numeric(as.character(temp.spec$mz))
temp.spec$intensity <- as.numeric(temp.spec$intensity)
temp.spec <- temp.spec[temp.spec$intensity != 0,]
} else{
temp.spec <- NULL
}
list('info' = temp.info,
'spec' = temp.spec)
})
mz.idx <- grep("[Mm][Zz]", rownames(info.spec[[1]][[1]]))
rt.idx <-
grep("Time|TIME|time|RT|rt|Rt", rownames(info.spec[[1]][[1]]))
##fix bug in msp data from metAnalyzer
if (length(rt.idx) == 0) {
cat(crayon::yellow("The msp data are from MetAnalyzer software.\n"))
rt.idx <-
grep("NAME|Name|name", rownames(info.spec[[1]][[1]]))
##rt.idx is the name of peak
info.spec <- lapply(info.spec, function(x) {
info <- x[[1]]
mz <- as.numeric(info[mz.idx, 1])
rt <- as.character(info[rt.idx, 1])
info <- c(mz, rt)
names(info) <- c("mz", "rt")
x[[1]] <- info
x
})
} else{
info.spec <- lapply(info.spec, function(x) {
info <- x[[1]]
mz <- as.numeric(info[mz.idx, 1])
rt <- as.numeric(info[rt.idx, 1])
info <- c(mz, rt)
names(info) <- c("mz", "rt")
x[[1]] <- info
x
})
}
}
remove.idx <-
which(unlist(lapply(info.spec, function(x)
is.null(x[[2]]))))
if (length(remove.idx) > 0) {
info.spec <- info.spec[-remove.idx]
}
info.spec <- info.spec
}