#2

R/rawR.R

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+#' readSpectrum of a raw file
+#'
+#' @param rawfile the name of the Thermo Fisher Scietific raw file which
+#' the data are to be read from.  
+#' @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 <cp@fgz.ethz.ch> 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. 
+#'  
+#' @references \url{https://doi.org/10.5281/zenodo.2640013}
+#' 
+#' @aliases readSpectrum
+#' 
+#' @export readSpectrum
+#' 
+#' @return  peaklistSet, a nested list of \CRANpkg{protViz} peaklist objects.
+#' 
+#' @examples
+#' (rawfile <- file.path(path.package(package = 'rawR'), 'extdata',
+#'   'sample.raw'))
+#' 
+#' S <- readSpectrum(rawfile, scans = 1:9)
+#' 
+#' S[[1]]
+#'  
+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")
+
+    tfi <- tempfile(tmpdir=tmpdir)
+    tfo <- tempfile(tmpdir=tmpdir)
+    tfstdout <- tempfile(tmpdir=tmpdir)
+
+    cat(scans, file = tfi, sep="\n")
+
+    cmd <- exe
+
+    if (mono){
+        rvs <- system2("mono", args = c(shQuote(exe), shQuote(rawfile),
+                                        "scans", shQuote(tfi), shQuote(tfo)))
+    }else{
+        rvs <- system2(exe, args = c( shQuote(rawfile), "scans", shQuote(tfi),
+                                      shQuote(tfo)))
+    }
+
+    e <- new.env(); e$PeakList <- list()
+    source(tfo, local=TRUE)
+    unlink(c(tfi, tfo, tfstdout))
+
+    return(lapply(e$PeakList,
+                  function(x){class(x) <- c(class(x), 'peaklist'); x}))
+}

R/zzz.R

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+#R
+
+#
+#' @importFrom utils packageVersion
+.onAttach <- function(lib, pkg){
+	if(interactive()){
+		version <- packageVersion('rawR')
+		packageStartupMessage("Package 'rawR' version ", version)
+	  invisible()
+	}
+}