Merge pull request #58 from fgcz/master

Use @inheritParams v1.7.9

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rawrr
 Type: Package
 Title: Direct Access to Orbitrap Data and Beyond
-Version: 1.7.8
+Version: 1.7.9
 Authors@R: c(person("Christian", "Panse",
         email = "[email protected]",
         role = c("aut", "cre"),

R/rawrr.R

@@ -189,8 +189,8 @@ is.rawrrSpectrumSet <- function(x){
 
 #' read file header Information
 #'
-#' @param rawfile the name of the Thermo Fisher Scietific raw file
-#' @description The function extracts meta information from a given rawfile.
+#' @param rawfile the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.
+#' @description This function extracts the meta information from a given raw file.
 #' @author Tobias Kockmann and Christian Panse 2018, 2019, 2020.
 #' @references Thermo Fisher Scientific's NewRawfileReader C# code snippets
 #' \url{https://planetorbitrap.com/rawfilereader}.
@@ -221,7 +221,7 @@ readFileHeader <- function(rawfile){
 # readIndex-----
 #' Read scan index
 #'
-#' @param rawfile the name of the Thermo Fisher Scientific raw file.
+#' @inheritParams readFileHeader
 #' @param tmpdir defines the directory used to store temporary data generated by
 #' the .NET assembly \code{rawrr.exe}. The default uses \code{tempdir()}.
 #' 
@@ -279,11 +279,9 @@ readIndex <- function(rawfile, tmpdir=tempdir()){
 
 #' derive scans number which match a specified filter
 #'
-#' @param rawfile the name of the Thermo Fisher Scietific raw file
+#' @inheritParams readIndex
 #' @param filter scan filter string, e.g., \code{ms} or \code{ms2}
 #' @param precision mass precision, default is 10.
-#' @param tmpdir defines the directory used to store temporary data generated by
-#' the .NET assembly \code{rawrr.exe}. The default uses \code{tempdir()}.
 #'
 #' @return a vecntor of integer values.
 filter <- function(rawfile, filter = "ms", precision = 10, tmpdir=tempdir()){
@@ -466,10 +464,8 @@ sampleFilePath <- function(){
 #' @description The function derives spectra of a given raw file and a given
 #' vector of scan numbers.
 #' 
-#' @param rawfile the name of the Thermo Fisher Scientific raw file.
+#' @inheritParams readIndex
 #' @param scan a vector of requested scan numbers.
-#' @param tmpdir defines the directory used to store temporary data generated by
-#' the .NET assembly \code{rawrr.exe}. The default uses \code{tempdir()}.
 #' @param validate boolean default is \code{FALSE}.
 #' @param mode if \code{mode = "barebone"} only mZ, intensity, pepmass, rtinseconds
 #' and charge state is returned. As default mode is \code{""}.
@@ -665,7 +661,7 @@ Please check the debug files:\n\t%s\n\t%s\nand the System Requirements",
 # readChromatogram ---------
 #' Extracts chromatographic data from a raw file.
 #'
-#' @param rawfile the file name.
+#' @inheritParams readFileHeader
 #' @param mass a vector of mass values iff \code{type = 'xic'}.
 #' @param tol mass tolerance in ppm iff \code{type = 'xic'}.
 #' @param filter defines the scan filter, default is \code{filter="ms"} if a
@@ -1423,11 +1419,9 @@ auc.rawrrChromatogram <- function(x){
 # readTrailer ---------
 #' Read and extract scan trailer from TFS raw files.
 #'
-#' @param rawfile the name of the Thermo Fisher Scientific raw file.
+#' @inheritParams readIndex
 #' @param label if NULL; the function scans for all available labels.
 #' @param verbose print message of temp files; default is \code{FALSE}.
-#' @param tmpdir defines the directory used to store temporary data generated by
-#' the .NET assembly \code{rawrr.exe}. The default uses \code{tempdir()}.
 #'
 #' @return an vector of trailers or values of a given trailer. Of note,
 #' the values are usually returned as a character.