diff --git a/DESCRIPTION b/DESCRIPTION index 70fb262..571c9ca 100644 --- a/DESCRIPTION +++ b/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 = "cp@fgcz.ethz.ch", role = c("aut", "cre"), diff --git a/R/rawrr.R b/R/rawrr.R index f47cee8..5486107 100644 --- a/R/rawrr.R +++ b/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. diff --git a/man/filter.Rd b/man/filter.Rd index 004e33b..a694813 100644 --- a/man/filter.Rd +++ b/man/filter.Rd @@ -7,7 +7,7 @@ filter(rawfile, filter = "ms", precision = 10, tmpdir = tempdir()) } \arguments{ -\item{rawfile}{the name of the Thermo Fisher Scietific raw file} +\item{rawfile}{the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.} \item{filter}{scan filter string, e.g., \code{ms} or \code{ms2}} diff --git a/man/readChromatogram.Rd b/man/readChromatogram.Rd index d7bec01..a4b27b3 100644 --- a/man/readChromatogram.Rd +++ b/man/readChromatogram.Rd @@ -7,7 +7,7 @@ readChromatogram(rawfile, mass = NULL, tol = 10, filter = "ms", type = "xic") } \arguments{ -\item{rawfile}{the file name.} +\item{rawfile}{the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.} \item{mass}{a vector of mass values iff \code{type = 'xic'}.} diff --git a/man/readFileHeader.Rd b/man/readFileHeader.Rd index 32e29e3..bcd19f2 100644 --- a/man/readFileHeader.Rd +++ b/man/readFileHeader.Rd @@ -7,7 +7,7 @@ readFileHeader(rawfile) } \arguments{ -\item{rawfile}{the name of the Thermo Fisher Scietific raw file} +\item{rawfile}{the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.} } \value{ A list object containing the following entries: RAW file version, @@ -21,7 +21,7 @@ Sample volume, Sample injection volume, Sample row number, Sample dilution factor, or Sample barcode. } \description{ -The function extracts meta information from a given rawfile. +This function extracts the meta information from a given raw file. } \examples{ rawrr::sampleFilePath() |> readFileHeader() diff --git a/man/readIndex.Rd b/man/readIndex.Rd index 40d36b4..4e0a22e 100644 --- a/man/readIndex.Rd +++ b/man/readIndex.Rd @@ -7,7 +7,7 @@ readIndex(rawfile, tmpdir = tempdir()) } \arguments{ -\item{rawfile}{the name of the Thermo Fisher Scientific raw file.} +\item{rawfile}{the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.} \item{tmpdir}{defines the directory used to store temporary data generated by the .NET assembly \code{rawrr.exe}. The default uses \code{tempdir()}.} diff --git a/man/readSpectrum.Rd b/man/readSpectrum.Rd index 49f65ca..f41a1b7 100644 --- a/man/readSpectrum.Rd +++ b/man/readSpectrum.Rd @@ -14,7 +14,7 @@ readSpectrum( ) } \arguments{ -\item{rawfile}{the name of the Thermo Fisher Scientific raw file.} +\item{rawfile}{the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.} \item{scan}{a vector of requested scan numbers.} diff --git a/man/readTrailer.Rd b/man/readTrailer.Rd index 1e0e1c3..3dbb5f2 100644 --- a/man/readTrailer.Rd +++ b/man/readTrailer.Rd @@ -7,7 +7,7 @@ readTrailer(rawfile, label = NULL, tmpdir = tempdir(), verbose = FALSE) } \arguments{ -\item{rawfile}{the name of the Thermo Fisher Scientific raw file.} +\item{rawfile}{the name of the raw file containing the mass spectrometry data from the Thermo Fisher Scientific instrument.} \item{label}{if NULL; the function scans for all available labels.}