Fixing missing or outdated documentation

R/SpectrumMethods.R

@@ -228,21 +228,38 @@ setMethod("normalize", c("RmbSpectrum2List"), function(object, ...)
 		})
 
 
-
+#' Add a mass shift to a spectrum
+#' 
+#' @param e1 a `MSnbase::Spectrum` object
+#' @param e2 a numeric mass shift
+#' 
 setMethod("+", c("Spectrum", "numeric"), function(e1, e2) 
 		{
 			e1@mz <- e1@mz + e2
 			return(e1)
 		}) 
 
 
-
+#' Add a negative mass shift to a spectrum
+#' 
+#' @param e1 a `MSnbase::Spectrum` object
+#' @param e2 a numeric mass shift
+#' 
 setMethod("-", c("Spectrum", "numeric"), function(e1, e2) 
 		{
 			e1@mz <- e1@mz - e2
 			return(e1)
 		}) 
 
+#' Add a mass shift to a list of spectra
+#' 
+#' Shifts both `parent` and `children` spectra of the `RmbSpectraSet` by the 
+#' same mass.
+#' 
+#' @param e1 a `RmbSpectraSet` object containing zero or more `children` spectra
+#'  and a `parent` spectrum
+#' @param e2 a numeric mass shift
+#' 
 setMethod("+", c("RmbSpectraSet", "ANY"), function(e1, e2)
 		{
 			e1@parent <- e1@parent + e2
@@ -251,6 +268,15 @@ setMethod("+", c("RmbSpectraSet", "ANY"), function(e1, e2)
 			e1
 		})
 
+#' Add a negative mass shift to a list of spectra
+#' 
+#' Shifts both `parent` and `children` spectra of the `RmbSpectraSet` by the 
+#' same mass.
+#' 
+#' @param e1 a `RmbSpectraSet` object containing zero or more `children` spectra
+#'  and a `parent` spectrum
+#' @param e2 a numeric mass shift
+#' 
 setMethod("-", c("RmbSpectraSet", "ANY"), function(e1, e2)
 		{
 			e1@parent <- e1@parent - e2
@@ -260,6 +286,13 @@ setMethod("-", c("RmbSpectraSet", "ANY"), function(e1, e2)
 		})
 
 
+#' Add a mass shift to a list of spectra
+#' 
+#' Shifts all spectra in a `RmbSpectrum2List` by the same mass
+#' 
+#' @param e1 a `RmbSpectrum2List` object containing zero or more `RmbSpectrum2` spectra
+#' @param e2 a numeric mass shift
+#' 
 setMethod("+", c("RmbSpectrum2List", "ANY"), function(e1, e2)
 		{
 			for(n in seq_len(length(e1)))
@@ -268,6 +301,13 @@ setMethod("+", c("RmbSpectrum2List", "ANY"), function(e1, e2)
 		})
 
 
+#' Add a negative mass shift to a list of spectra
+#' 
+#' Shifts all spectra in a `RmbSpectrum2List` by the same mass
+#' 
+#' @param e1 a `RmbSpectrum2List` object containing zero or more `RmbSpectrum2` spectra
+#' @param e2 a numeric mass shift
+#' 
 setMethod("-", c("RmbSpectrum2List", "ANY"), function(e1, e2)
 		{
 			for(n in seq_len(length(e1)))

R/buildRecord.R

@@ -29,6 +29,9 @@
 #' @param mbdata list
 #' The information data block for the record header, as stored in
 #' \code{mbdata_relisted} after loading an infolist.
+#' @param analyticalInfo A list containing information for the `AC$` section of
+#'  a MassBank record, with elements `ai, ac_lc, ac_ms` for general, LC and MS
+#'  info respectively.
 #' @param additionalPeaks data.frame
 #' If present, a table with additional peaks to add into the spectra.
 #' 		As loaded with \code{\link{addPeaks}}.

R/createMassBank.R

@@ -1488,12 +1488,25 @@ annotator.default <- function(annotation, formulaTag)
 #' @export
 setGeneric("toMassbank", function(o, ...) standardGeneric("toMassbank"))
 
+
+#' Convert spectra from a `RmbSpectraSet` object to MassBank records
+#' 
+#' @param addAnnotation `logical`, whether to add peak annotations (putative formulas) to the record.
+#' 
+#' @returns A list of character vectors with the MassBank records
+#' 
 #' @export
 setMethod("toMassbank", "RmbSpectraSet", function(o, addAnnotation = getOption("RMassBank")$add_annotation)
     {
       lapply(o@children, function(s) toMassbank(s, addAnnotation))
     })
 
+#' Convert a `RmbSpectrum2` object to a MassBank record
+#' 
+#' @param addAnnotation `logical`, whether to add peak annotations (putative formulas) to the record.
+#' 
+#' @returns A character vector with the MassBank record
+#' 
 #' @export
 setMethod("toMassbank", "RmbSpectrum2", function(o, addAnnotation = getOption("RMassBank")$add_annotation)
     {

R/leMsMs.r

@@ -57,6 +57,8 @@ archiveResults <- function(w, fileName, settings = getOption("RMassBank"))
 #'        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".
+#' @param filetable If including step 1 (data extraction), a `filetable` argument
+#'        to be passed to \code{\link{msmsRead}}.
 #' @param findPeaksArgs A list of arguments that will be handed to the xcms-method findPeaks via do.call
 #' @param plots A parameter that determines whether the spectra should be plotted or not (This parameter is only used for the xcms-method)
 #' @param precursorscan.cf Whether to fill precursor scans. To be used with files which for
@@ -1292,7 +1294,7 @@ setMethod("cleanElnoise", c("RmbSpectraSet", noise="numeric", width="numeric"),
 #' sp@@good <- c(TRUE, TRUE, TRUE, FALSE, FALSE)
 #' sp@@precursorMz <- 600
 #' sp_checked <- problematicPeaks(sp)
-#' stopifnot(sum(getData(sp_checked)$problematicPeaks) == 2))
+#' stopifnot(sum(getData(sp_checked)$problematicPeaks) == 2)
 #' @export
 problematicPeaks <- function(sp)
 {
@@ -1330,7 +1332,6 @@ problematicPeaks <- function(sp)
 #' Generates a list of intense unmatched peaks for further review (the "failpeak list") and exports it if the archive name is given.
 #' 
 #' @param w \code{msmsWorkspace} to analyze. 
-#' @param mode Processing mode (pH etc)
 #' @param archivename Base name of the archive to write to (for "abc" the exported failpeaks list will be "abc_Failpeaks.csv").
 #' if the compoundlist is complete, "tentative", if at least a formula is present or "unknown"
 #' if the only know thing is the m/z
@@ -1764,6 +1765,7 @@ filterPeakSatellites <- function(peaks, filterSettings = getOption("RMassBank")$
 #' @param progressbar The progress bar callback to use. Only needed for specialized
 #'  applications.	Cf. the documentation of \code{\link{progressBarHook}} for usage.
 #' @param filterSettings Settings for filtering data. Refer to\code{\link{analyzeMsMs}} for settings.
+#' @param mode for `reanalyzeFailpeak`, the `mode` (adduct) of the analyzed spectrum.
 #' @return The aggregate data frame extended by the columns:
 #' #' \item{reanalyzed.???}{If reanalysis (step 7) has already been processed: matching values from the reanalyzed peaks}
 #' \item{matchedReanalysis}{Whether reanalysis has matched (\code{TRUE}), not matched(\code{FALSE}) or has not been conducted for the peak(\code{NA}).}
@@ -2150,7 +2152,7 @@ filterMultiplicity <- function(w, archivename=NA, mode="pH", recalcBest = TRUE,
 #' to the \code{spec$peaksMatched} table. However, only minimal information needed for
 #' recalibration is returned. 
 #' 
-#' @usage  recalibrate.addMS1data(spec,mode="pH", recalibrateMS1Window = 
+#' @usage  recalibrate.addMS1data(spec, recalibrateMS1Window = 
 #' 				getOption("RMassBank")$recalibrateMS1Window)
 #' @param spec A \code{msmsWorkspace} or \code{RmbSpectraSetList} containing spectra for which MS1 "peaks" should be "constructed". 
 #' @param recalibrateMS1Window Window width to look for MS1 peaks to recalibrate (in ppm).

R/leMsmsRaw.R

@@ -29,18 +29,6 @@ NULL # This is required so that roxygen knows where the first manpage starts
 #' 
 #' @note \code{findMsMs.direct} is deactivated
 #' 
-## # @usage findMsMsHR(fileName, cpdID, mode="pH",confirmMode =0, useRtLimit = TRUE,
-## # 		ppmFine = getOption("RMassBank")$findMsMsRawSettings$ppmFine,
-## # 		mzCoarse = getOption("RMassBank")$findMsMsRawSettings$mzCoarse,
-## # 		fillPrecursorScan = getOption("RMassBank")$findMsMsRawSettings$fillPrecursorScan,
-## # 		rtMargin = getOption("RMassBank")$rtMargin,
-## # 		deprofile = getOption("RMassBank")$deprofile,
-## # 		headerCache = NULL,
-## # 		peaksCache = NULL)
-## # 		
-## # findMsMsHR.mass(msRaw, mz, limit.coarse, limit.fine, rtLimits = NA, maxCount = NA,
-## # 		headerCache = NULL, fillPrecursorScan = FALSE,
-## # 		deprofile = getOption("RMassBank")$deprofile, peaksCache = NULL, cpdID = NA)
 #' 
 #' 
 #' @aliases findMsMsHR.mass findMsMsHR
@@ -85,6 +73,10 @@ NULL # This is required so that roxygen knows where the first manpage starts
 #' 			used (cf. \code{\link{deprofile}}) 
 #' @param diaWindows A data frame with columns \code{precursorMz}, \code{mzMin}, \code{mzMax} which specifies the precursor and 
 #'      window size of each window for DIA acquisition.
+#' @param enforcePolarity If TRUE, scans are filtered for the given `mode`'s polarity when
+#'      finding the target spectrum.
+#' @param polarity If set (for ?findMsMsHR.mass), scans are filtered for the given `mode`'s polarity when
+#'      finding the target spectrum.
 #' @return	An \code{RmbSpectraSet} (for \code{findMsMsHR}). Contains parent MS1 spectrum (\code{@@parent}), a block of dependent MS2 spectra ((\code{@@children})
 #' 			and some metadata (\code{id},\code{mz},\code{name},\code{mode} in which the spectrum was acquired.
 #' 
@@ -106,7 +98,9 @@ NULL # This is required so that roxygen knows where the first manpage starts
 #' @author Michael A. Stravs, Eawag <michael.stravs@@eawag.ch>
 #' @seealso findEIC
 #' @export
-findMsMsHR <- function(fileName = NULL, msRaw = NULL, cpdID, mode="pH",confirmMode =0, useRtLimit = TRUE,
+findMsMsHR <- function(
+    fileName = NULL, msRaw = NULL, cpdID, mode="pH", 
+    confirmMode = 0, useRtLimit = TRUE,
 		ppmFine = getOption("RMassBank")$findMsMsRawSettings$ppmFine,
 		mzCoarse = getOption("RMassBank")$findMsMsRawSettings$mzCoarse,
 		fillPrecursorScan = getOption("RMassBank")$findMsMsRawSettings$fillPrecursorScan,
@@ -969,6 +963,15 @@ read.msp <- function(file){
 #' 			freshly from \code{msRaw} for every compound.
 #' @param peaksCache If present, the complete output of \code{mzR::peaks(msRaw)}. This speeds up the lookup
 #' 			if multiple compounds should be searched in the same file.
+#' @param polarity If a value is given, scans are filtered to this polarity before EIC
+#'  extraction. Valid values are 1 for positive, 0 for negative (according to mzR), or a RMassBank
+#'  `mode` (e.g. `pH, pM, mH...`) from which the polarity can be derived.
+#' @param msLevel Which MS level to target for EIC extraction. By default this is 1; level 2
+#'  can be used to extract the EIC of fragments for a specific precursor or to extract EICs
+#'  from DIA data.
+#' @param precursor Which precursor to target for EIC extraction. If `NULL`, the scans are not 
+#'  filtered by precursor. Use this only for `msLevel != 1`. If a `precursor` filter is set for 
+#'  `msLevel == 1`, all scans will be filtered out.
 #' @param floatingRecalibration 
 #' 			A fitting function that \code{predict()}s a mass shift based on the retention time. Can be used
 #' 			if a lockmass calibration is known (however you have to build the calibration yourself.)

R/log_wrapper.R

@@ -4,6 +4,9 @@ NULL
 #' Pass arguments to logger::log_info using custom RMassBank-logging settings
 #'
 #' The logging file to be used can be specified by the user in the \code{logging_file} field of \code{settings.ini}
+#'
+#' @param ... The log message, as for `logger::log_...` functions
+#'
 #' @seealso logger::log_info
 #' @author pstahlhofen
 #' @export
@@ -14,6 +17,9 @@ rmb_log_info <- function(...) {
 #' Pass arguments to logger::log_trace using custom RMassBank-logging settings
 #'
 #' The logging file to be used can be specified by the user in the \code{logging_file} field of \code{settings.ini}
+#' 
+#' @param ... The log message, as for `logger::log_...` functions
+#' 
 #' @seealso logger::log_trace
 #' @author pstahlhofen
 #' @export
@@ -24,6 +30,9 @@ rmb_log_trace <- function(...) {
 #' Pass arguments to logger::log_debug using custom RMassBank-logging settings
 #'
 #' The logging file to be used can be specified by the user in the \code{logging_file} field of \code{settings.ini}
+#' 
+#' @param ... The log message, as for `logger::log_...` functions
+#' 
 #' @seealso logger::log_debug
 #' @author pstahlhofen
 #' @export
@@ -34,6 +43,9 @@ rmb_log_debug <- function(...) {
 #' Pass arguments to logger::log_warn using custom RMassBank-logging settings
 #'
 #' The logging file to be used can be specified by the user in the \code{logging_file} field of \code{settings.ini}
+#' 
+#' @param ... The log message, as for `logger::log_...` functions
+#' 
 #' @seealso logger::log_warn
 #' @author pstahlhofen
 #' @export
@@ -44,6 +56,9 @@ rmb_log_warn <- function(...) {
 #' Pass arguments to logger::log_success using custom RMassBank-logging settings
 #'
 #' The logging file to be used can be specified by the user in the \code{logging_file} field of \code{settings.ini}
+#' 
+#' @param ... The log message, as for `logger::log_...` functions
+#' 
 #' @seealso logger::log_success
 #' @author pstahlhofen
 #' @export
@@ -54,6 +69,9 @@ rmb_log_success <- function(...) {
 #' Pass arguments to logger::log_error using custom RMassBank-logging settings
 #'
 #' The logging file to be used can be specified by the user in the \code{logging_file} field of \code{settings.ini}
+#' 
+#' @param ... The log message, as for `logger::log_...` functions
+#' 
 #' @seealso logger::log_error
 #' @author pstahlhofen
 #' @export
@@ -64,6 +82,9 @@ rmb_log_error <- function(...) {
 #' Pass arguments to logger::log_fatal using custom RMassBank-logging settings
 #'
 #' The logging file to be used can be specified by the user in the \code{logging_file} field of \code{settings.ini}
+#' 
+#' @param ... The log message, as for `logger::log_...` functions
+#' 
 #' @seealso logger::log_fatal
 #' @author pstahlhofen
 #' @export