docs: restructure documentation

R/AllGenerics.R

@@ -5,42 +5,32 @@ NULL
 setMethod("bin", "numeric", MsCoreUtils::bin)
 setGeneric("combinePeaks", function(object, ...)
            standardGeneric("combinePeaks"))
-#' @rdname hidden_aliases
 setGeneric("containsMz", function(object, ...)
     standardGeneric("containsMz"))
-#' @rdname hidden_aliases
 setGeneric("containsNeutralLoss", function(object, ...)
     standardGeneric("containsNeutralLoss"))
 setGeneric("dataStorageBasePath", function(object, ...)
     standardGeneric("dataStorageBasePath"))
 setGeneric("dataStorageBasePath<-", function(object, ..., value)
     standardGeneric("dataStorageBasePath<-"))
-#' @rdname hidden_aliases
 setGeneric("dropNaSpectraVariables", function(object, ...)
     standardGeneric("dropNaSpectraVariables"))
-#' @rdname hidden_aliases
 setGeneric("entropy", function(object, ...)
   standardGeneric("entropy"))
-#' @rdname hidden_aliases
 setGeneric("export", function(object, ...)
     standardGeneric("export"))
 setGeneric("filterFourierTransformArtefacts", function(object, ...)
     standardGeneric("filterFourierTransformArtefacts"))
-#' @rdname neutralLoss
 setGeneric("neutralLoss", function(object, param, ...)
     standardGeneric("neutralLoss"))
-#' @rdname hidden_aliases
 setGeneric("pickPeaks", function(object, ...)
     standardGeneric("pickPeaks"))
 setGeneric("plotSpectraMirror", function(x, y, ...)
     standardGeneric("plotSpectraMirror"))
-#' @rdname hidden_aliases
 setGeneric("replaceIntensitiesBelow", function(object, threshold = min, ...)
     standardGeneric("replaceIntensitiesBelow"))
-#' @rdname hidden_aliases
 setGeneric("reset", function(object, ...)
     standardGeneric("reset"))
-#' @rdname hidden_aliases
 setGeneric("selectSpectraVariables", function(object, ...)
     standardGeneric("selectSpectraVariables"))
 setGeneric("Spectra", function(object, ...) standardGeneric("Spectra"))

R/MsBackend.R

@@ -702,7 +702,7 @@
 #'
 #' The parameters are:
 #' - `object`: an instance of the `MsBackendMzR` class.
-#' - `x`: the [Spectra-class] object to be exported.
+#' - `x`: the [Spectra] object to be exported.
 #' - `file`: `character` with the (full) output file name(s). Should be
 #'   of length 1 or equal `length(x)`. If a single file is specified, all
 #'   spectra are exported to that file. Alternatively it is possible to specify
@@ -715,7 +715,7 @@
 #'   backend and if `dataOrigin(x)` contains the original MS data file names.
 #' - `BPPARAM`: parallel processing settings.
 #'
-#' See examples in [Spectra-class] or the vignette for more details and
+#' See examples in [Spectra] or the vignette for more details and
 #' examples.
 #'
 #' The `MsBackendMzR` ignores parameter `columns` of the `peaksData()`

R/Spectra-estimatePrecursorMz.R

@@ -55,6 +55,10 @@
 #'
 #' @author Mar Garcia-Aloy, Johannes Rainer
 #'
+#' @seealso
+#'
+#' [addProcessing()] for other data analysis and manipulation functions.
+#'
 #' @export
 #'
 #' @examples

R/Spectra-functions.R

@@ -207,7 +207,7 @@ NULL
 
 #' @export applyProcessing
 #'
-#' @rdname Spectra
+#' @rdname addProcessing
 applyProcessing <- function(object, f = processingChunkFactor(object),
                             BPPARAM = bpparam(), ...) {
     queue <- object@processingQueue
@@ -538,14 +538,14 @@ applyProcessing <- function(object, f = processingChunkFactor(object),
 
 #' @export concatenateSpectra
 #'
-#' @rdname Spectra
+#' @rdname combineSpectra
 concatenateSpectra <- function(x, ...) {
     .concatenate_spectra(unlist(unname(list(unname(x), ...))))
 }
 
 #' @export combineSpectra
 #'
-#' @rdname Spectra
+#' @rdname combineSpectra
 combineSpectra <- function(x, f = x$dataStorage, p = x$dataStorage,
                            FUN = combinePeaksData, ..., BPPARAM = bpparam()) {
     if (!is.factor(f))
@@ -622,7 +622,7 @@ combineSpectra <- function(x, f = x$dataStorage, p = x$dataStorage,
 
 #' @export joinSpectraData
 #'
-#' @rdname Spectra
+#' @rdname combineSpectra
 joinSpectraData <- function(x, y,
                             by.x = "spectrumId",
                             by.y,
@@ -685,7 +685,7 @@ joinSpectraData <- function(x, y,
 
 #' @export
 #'
-#' @rdname Spectra
+#' @rdname addProcessing
 processingLog <- function(x) {
     x@processing
 }
@@ -831,9 +831,7 @@ chunkapply <- function(x, FUN, ..., chunkSize = 1000L, chunks = factor()) {
     as.factor(rep(1:ceiling(len / chunkSize), each = chunkSize)[seq_len(len)])
 }
 
-#' @rdname Spectra
-#'
-#' @author Nir Shahaf, Johannes Rainer
+#' @rdname filterMsLevel
 #'
 #' @export
 deisotopeSpectra <-
@@ -845,9 +843,7 @@ deisotopeSpectra <-
                       substDefinition = im, charge = charge)
     }
 
-#' @rdname Spectra
-#'
-#' @author Nir Shahaf, Johannes Rainer
+#' @rdname filterMsLevel
 #'
 #' @export
 reduceSpectra <- function(x, tolerance = 0, ppm = 20) {
@@ -856,9 +852,7 @@ reduceSpectra <- function(x, tolerance = 0, ppm = 20) {
     addProcessing(x, .peaks_reduce, tolerance = tolerance, ppm = ppm)
 }
 
-#' @rdname Spectra
-#'
-#' @author Nir Shahaf
+#' @rdname filterMsLevel
 #'
 #' @export
 filterPrecursorMaxIntensity <- function(x, tolerance = 0, ppm = 20) {
@@ -891,9 +885,7 @@ filterPrecursorMaxIntensity <- function(x, tolerance = 0, ppm = 20) {
     x
 }
 
-#' @rdname Spectra
-#'
-#' @author Nir Shahaf
+#' @rdname filterMsLevel
 #'
 #' @export
 filterPrecursorIsotopes <-
@@ -926,9 +918,7 @@ filterPrecursorIsotopes <-
         x
 }
 
-#' @rdname Spectra
-#'
-#' @author Johannes Rainer
+#' @rdname addProcessing
 #'
 #' @export
 scalePeaks <- function(x, by = sum, msLevel. = uniqueMsLevels(x)) {
@@ -941,7 +931,7 @@ scalePeaks <- function(x, by = sum, msLevel. = uniqueMsLevels(x)) {
     x
 }
 
-#' @rdname Spectra
+#' @rdname filterMsLevel
 #'
 #' @export
 filterPrecursorPeaks <- function(object, tolerance = 0, ppm = 20,
@@ -992,6 +982,11 @@ filterPrecursorPeaks <- function(object, tolerance = 0, ppm = 20,
 #'   per file parallel processing if `f` or `chunkSize` is not defined.
 #'   Other on-disk backends: only if requested by the user.
 #'
+#' @param BPPARAM Parallel setup configuration. See [bpparam()] for more
+#'     information.
+#'
+#' @param object `Spectra` object.
+#'
 #' @param x `Spectra` object.
 #'
 #' @param chunkSize `integer` defining the size of chunks into which `x` should
@@ -1067,6 +1062,11 @@ filterPrecursorPeaks <- function(object, tolerance = 0, ppm = 20,
 #' For these, the `backendBpparam()` function will always return a
 #' `SerialParam()` independently on how parallel processing was defined.
 #'
+#' @param BPPARAM Parallel setup configuration. See [bpparam()] for more
+#'     information.
+#'
+#' @param object `Spectra` object.
+#'
 #' @param x `Spectra`.
 #'
 #' @param value `integer(1)` defining the chunk size.

R/Spectra-neutralLoss.R

@@ -87,6 +87,10 @@ setClassUnion("functionOrNull", c("function", "NULL"))
 #' Analysis in METLIN. Journal of the American Society for Mass Spectrometry.
 #' \doi{10.1021/jasms.1c00343}
 #'
+#' @seealso
+#'
+#' [addProcessing()] for other data analysis and manipulation functions.
+#'
 #' @examples
 #'
 #' ## Create a simple example Spectra object with some MS1, MS2 and MS3 spectra.