Add Todor and msmsRead.parallel

DESCRIPTION

@@ -72,4 +72,4 @@ Collate:
     'msmsRead.R'
     'Isotopic_Annotation.R'
     'zzz.R'
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1

NAMESPACE

@@ -113,6 +113,7 @@ export(toMassbank)
 export(toRMB)
 export(updateSettings)
 export(validate)
+export(msmsRead.parallel)
 exportClasses(mbWorkspace)
 exportClasses(msmsWorkspace)
 exportMethods(addProperty)

R/msmsRead.R

@@ -425,7 +425,7 @@ msmsRead.RAW <- function(w, xRAW = NULL, cpdids = NULL, mode, findPeaksArgs = NU
 #' @seealso \code{\link{msmsWorkspace-class}},
 #'     \code{\link{msmsWorkflow}}
 #' @author Michael Stravs, Eawag <michael.stravs@@eawag.ch>
-#' @author Erik Mueller, UFZ
+#' @author Todor Kondić, LCSB-ECI <todor.kondic@@uni.lu>
 #' @export
 msmsRead.parallel <- function(w,proc,outfile="",filetable = NULL, files = NULL, cpdids = NULL, 
                               readMethod, mode, confirmMode = FALSE, useRtLimit = TRUE, 

man/msmsRead.parallel.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/msmsRead.R
+\name{msmsRead.parallel}
+\alias{msmsRead.parallel}
+\title{Extracts and processes spectra from a specified file list, according to 
+loaded options and given parameters.}
+\usage{
+msmsRead.parallel(w, proc, outfile = "", filetable = NULL,
+  files = NULL, cpdids = NULL, readMethod, mode, confirmMode = FALSE,
+  useRtLimit = TRUE, Args = NULL, settings = getOption("RMassBank"),
+  progressbar = "progressBarHook", MSe = FALSE, plots = FALSE)
+}
+\arguments{
+\item{w}{A \code{msmsWorkspace} to work with.}
+
+\item{proc}{Number of processes to be used to exec the function.}
+
+\item{outfile}{Filepath of the logging file. Defaults to stdout ("").}
+
+\item{filetable}{The path to a .csv-file that contains the columns
+"Files" and "ID" supplying the relationships between files and
+compound IDs. Either this or the parameter "files" need to be
+specified.}
+
+\item{files}{A vector or list containing the filenames of the files
+that are to be read as spectra.  For the IDs to be inferred
+from the filenames alone, there need to be exactly 2
+underscores.}
+
+\item{cpdids}{A vector or list containing the compound IDs of the
+files that are to be read as spectra.  The ordering of this and
+\code{files} implicitly assigns each ID to the corresponding
+file.  If this is supplied, then the IDs implicitly named in
+the filenames are ignored.}
+
+\item{readMethod}{Several methods are available to get peak lists
+from the files.  Currently supported are "mzR", "xcms",
+"MassBank" and "peaklist".  The first two read MS/MS raw data,
+and differ in the strategy used to extract peaks. MassBank will
+read existing records, so that e.g. a recalibration can be
+performed, and "peaklist" just requires a CSV with two columns
+and the column header "mz", "int".}
+
+\item{mode}{\code{"pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA"} for
+different ions ([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-,
+[M+FA]-).}
+
+\item{confirmMode}{Defaults to false (use most intense
+precursor). Value 1 uses the 2nd-most intense precursor for a
+chosen ion (and its data-dependent scans) , etc.}
+
+\item{useRtLimit}{Whether to enforce the given retention time
+window.}
+
+\item{Args}{A list of arguments that will be handed to the
+xcms-method findPeaks via do.call}
+
+\item{settings}{Options to be used for processing. Defaults to the
+options loaded via \code{\link{loadRmbSettings}} et al. Refer
+to there for specific settings.}
+
+\item{progressbar}{The progress bar callback to use. Only needed
+for specialized applications.  Cf. the documentation of
+\code{\link{progressBarHook}} for usage.}
+
+\item{MSe}{A boolean value that determines whether the spectra were
+recorded using MSe or not}
+
+\item{plots}{A boolean value that determines whether the
+pseudospectra in XCMS should be plotted}
+}
+\value{
+The \code{msmsWorkspace} with msms-spectra read.
+}
+\description{
+The filenames of the raw LC-MS runs are read from the array \code{files} 
+in the global enviroment.
+See the vignette \code{vignette("RMassBank")} for further details about the
+workflow.
+}
+\seealso{
+\code{\link{msmsWorkspace-class}},
+    \code{\link{msmsWorkflow}}
+}
+\author{
+Michael Stravs, Eawag <michael.stravs@eawag.ch>
+
+Todor Kondić, LCSB-ECI <todor.kondic@uni.lu>
+}