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@@ -1,17 +1,23 @@ | ||
#' readSpectrum of a raw file | ||
#' Read a Set of Spectra | ||
#' | ||
#' @param rawfile the name of the Thermo Fisher Scietific raw file which | ||
#' the data are to be read from. | ||
#' @param rawfile the name of the Thermo Fisher Scietific raw file. | ||
#' @param scans a vector of requested scan numbers. | ||
#' @param tmpdir a non-empty character vector giving the directory name; default | ||
#' uses \code{tempdir()}. | ||
#' @author Christian Panse <[email protected]> 2018, 2019, 2020 | ||
#' @author Tobias Kockmann and Christian Panse <[email protected]> 2018, 2019, 2020 | ||
#' | ||
#' @description the function reads scan information of a given set of scan | ||
#' number using a dot net interface and the ThermoFisher NewRawFileReader | ||
#' libraries. | ||
#' @description the function reads scan information, e.g., charge, mZ, | ||
#' or intensity of a given set of scan numbers using a dot net interface and | ||
#' the ThermoFisher NewRawFileReader libraries. | ||
#' | ||
#' @references \url{https://doi.org/10.5281/zenodo.2640013} | ||
#' @seealso Thermo Fisher NewRawfileReader C# code snippets | ||
#' \url{https://planetorbitrap.com/rawfilereader}. | ||
#' | ||
#' @references \itemize{ | ||
#' \item{\url{https://doi.org/10.5281/zenodo.2640013}} | ||
#' \item{the R function 1st appeared in | ||
#' \url{https://doi.org/10.1021/acs.jproteome.8b00173}} | ||
#' } | ||
#' | ||
#' @aliases readSpectrum | ||
#' | ||
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@@ -26,11 +32,25 @@ | |
#' S <- readSpectrum(rawfile, scans = 1:9) | ||
#' | ||
#' S[[1]] | ||
#' | ||
#' names(S[[1]]) | ||
#' | ||
#' .plot.peaklist <- function(x, ...){ | ||
#' plot(x$mZ, x$intensity, type='h') | ||
#' labels <- na.omit(lapply(x, function(y){if (length(y)==1){y}else{NA}})) | ||
#' legend("topright", paste(names(labels), labels, sep=": "), ...) | ||
#' } | ||
#' | ||
readSpectrum <- function(rawfile, scans, tmpdir=tempdir()){ | ||
mono <- if(Sys.info()['sysname'] %in% c("Darwin", "Linux")) TRUE else FALSE | ||
exe <- file.path(path.package(package = "rawR"), "exec", "rawR.exe") | ||
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if (!file.exists(rawfile)){ | ||
warning('file not available. return.') | ||
return | ||
} | ||
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tfi <- tempfile(tmpdir=tmpdir) | ||
tfo <- tempfile(tmpdir=tmpdir) | ||
tfstdout <- tempfile(tmpdir=tmpdir) | ||
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@@ -54,3 +74,74 @@ readSpectrum <- function(rawfile, scans, tmpdir=tempdir()){ | |
return(lapply(e$PeakList, | ||
function(x){class(x) <- c(class(x), 'peaklist'); x})) | ||
} | ||
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#' read file header Information | ||
#' | ||
#' @param rawfile the name of the Thermo Fisher Scietific raw file | ||
#' @param mono enviroment | ||
#' @param exe path of the executable. | ||
#' @param mono_path default. | ||
#' @param argv arguments, default. | ||
#' @param system2_call system2 call, default. | ||
#' @param method instrument vendor | ||
#' @description The function extracts some meta information from a given rawfile. | ||
#' The R code output is parsed by the function and a list object is returned. | ||
#' @author Tobias Kockmann and Christian Panse 2018, 2019, 2020 | ||
#' @seealso Thermo Fisher NewRawfileReader C# code snippets | ||
#' \url{https://planetorbitrap.com/rawfilereader}. | ||
#' | ||
#' @return a list object | ||
#' @export readFileHeader | ||
#' | ||
#' @examples | ||
#' (rawfile <- file.path(path.package(package = 'rawR'), 'extdata', | ||
#' 'sample.raw')) | ||
#' | ||
#' M <- readFileHeader(rawfile) | ||
readFileHeader <- function(rawfile, | ||
mono = if(Sys.info()['sysname'] %in% c("Darwin", "Linux")) TRUE else FALSE, | ||
exe = file.path(path.package(package = "rawR"), "exec", "rawR.exe"), | ||
mono_path = "", | ||
argv = "infoR", | ||
system2_call = TRUE, | ||
method = "thermo"){ | ||
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if (!file.exists(rawfile)){ | ||
warning('file not available. return.') | ||
return | ||
} | ||
if(system2_call && method == 'thermo'){ | ||
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tf <- tempfile(fileext = '.R') | ||
tf.err <- tempfile(fileext = '.err') | ||
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# message(paste("system2 is writting to tempfile ", tf, "...")) | ||
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if (mono){ | ||
rvs <- system2("mono", args = c(exe, shQuote(rawfile | ||
), argv), | ||
stdout = tf) | ||
}else{ | ||
rvs <- system2(exe, args = c(shQuote(rawfile | ||
), argv), | ||
stderr = tf.err, | ||
stdout = tf) | ||
} | ||
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if (rvs == 0){ | ||
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try({ | ||
source(tf) | ||
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#message(paste("unlinking", tf, "...")) | ||
#unlink(tf) | ||
return(e$info) | ||
}, NULL) | ||
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# unlink(tfstdout) | ||
return(rv) | ||
} | ||
} | ||
NULL | ||
} |