docs: convert documentation to markdown format

R/DataClasses.R

@@ -1738,7 +1738,7 @@ setClass("MsFeatureData", contains = c("environment"),
 #' - [overlappingFeatures()] identify features that are overlapping or close
 #'   in the m/z - rt space (see respective help page).
 #'
-#' - [quantify()]: extract feature intensities and put them, along
+#' - [xcms::quantify()]: extract feature intensities and put them, along
 #'   with feature definitions and phenodata information, into a
 #'   [SummarizedExperiment::SummarizedExperiment()]. See help page for details.
 #'

R/XcmsExperiment.R

@@ -1,7 +1,7 @@
 #' @title Next Generation `xcms` Result Object
 #'
 #' @aliases XcmsExperiment-class show,XcmsExperiment-method filterChromPeaks
-#' @aliases featureArea
+#' @aliases featureArea quantify
 #'
 #' @description
 #'
@@ -1216,7 +1216,8 @@ setMethod(
                  colnames(chromPeaks)))
             stop("'chromPeaks' lacks one or more of the required colums ",
                  "\"mzmin\", \"mzmax\", \"rtmin\" and \"rtmax\".")
-        chromPeaks <- chromPeaks[, c("mzmin", "mzmax", "rtmin", "rtmax")]
+        chromPeaks <- chromPeaks[, c("mzmin", "mzmax", "rtmin", "rtmax"),
+                                 drop = FALSE]
         if (!all(samples %in% seq_along(object)))
             stop("'samples' out of bounds")
         if (hasFeatures(object))

R/do_findChromPeaks-functions.R

@@ -2379,14 +2379,14 @@ do_findPeaks_MSW <- function(mz, int, snthresh = 3,
 ## }
 
 ## Tuned from the original code.
-#' @param peaks. \code{matrix} or \code{data.frame} with peaks for which
-#' isotopes should be predicted. Required columns are \code{"mz"},
-#' \code{"mzmin"}, \code{"mzmax"}, \code{"scmin"}, \code{"scmax"},
-#' \code{"intb"} and \code{"scale"}.
-#'
-#' @return a \code{matrix} with columns \code{"mz"}, \code{"mzmin"},
-#' \code{"mzmax"}, \code{"scmin"}, \code{"scmax"}, \code{"length"} (always -1),
-#' \code{"intensity"} (always -1) and \code{"scale"}.
+#' @param peaks. `matrix` or `data.frame` with peaks for which
+#' isotopes should be predicted. Required columns are `"mz"`,
+#' `"mzmin"`, `"mzmax"`, `"scmin"`, `"scmax"`,
+#' `"intb"` and `"scale"`.
+#'
+#' @return a `matrix` with columns `"mz"`, `"mzmin"`,
+#' `"mzmax"`, `"scmin"`, `"scmax"`, `"length"` (always -1),
+#' `"intensity"` (always -1) and `"scale"`.
 #' @noRd
 do_define_isotopes <- function(peaks., maxCharge = 3, maxIso = 5,
                                mzIntervalExtension = TRUE) {
@@ -2430,8 +2430,8 @@ do_define_isotopes <- function(peaks., maxCharge = 3, maxIso = 5,
 
 #' @param peaks. see do_define_isotopes
 #'
-#' @param polarity character(1) defining the polarity, either \code{"positive"}
-#'     or \code{"negative"}.
+#' @param polarity character(1) defining the polarity, either `"positive"`
+#'     or `"negative"`.
 #'
 #' @note
 #'

R/functions-MsFeatureData.R

@@ -4,7 +4,7 @@
 #' Validates a 'chromPeaks' matrix or data.frame and ensures that it contains all
 #' required columns and that all columns are of numeric data type.
 #'
-#' @return \code{TRUE} or a \code{character} with the error message.
+#' @return `TRUE` or a `character` with the error message.
 #'
 #' @noRd
 .validChromPeaksMatrix <- function(x) {
@@ -62,7 +62,7 @@
 #'
 #' @author Johannes Rainer
 #'
-#' @return \code{TRUE} if object is valid, or a message with the error message.
+#' @return `TRUE` if object is valid, or a message with the error message.
 #'
 #' @noRd
 validateMsFeatureData <- function(x) {
@@ -157,12 +157,12 @@ validateMsFeatureData <- function(x) {
 #' @description Filter chromPeaks and sync them with with the present
 #'     featureDefinitions, i.e. update their peakidx column or remove them.
 #'
-#' @param x A \code{MsFeatureData} or an \code{XCMSnExp} object.
+#' @param x A `MsFeatureData` or an `XCMSnExp` object.
 #'
-#' @param idx \code{numeric} with the indices of the chromatographic peaks to
+#' @param idx `numeric` with the indices of the chromatographic peaks to
 #'     keep.
 #'
-#' @return A \code{MsFeatureData}.
+#' @return A `MsFeatureData`.
 #'
 #' @author Johannes Rainer
 #'

R/functions-OnDiskMSnExp.R

@@ -10,8 +10,8 @@
 #' @param param A class extending Param containing all parameters for the
 #'     peak detection method.
 #'
-#' @return a list of length 2, \code{peaks} containing a matrix with the
-#'     identified peaks and \code{date} the time stamp when the peak detection
+#' @return a list of length 2, `peaks` containing a matrix with the
+#'     identified peaks and `date` the time stamp when the peak detection
 #'     was started.
 #'
 #' @noRd
@@ -42,8 +42,8 @@ findChromPeaks_OnDiskMSnExp <- function(object, method = "centWave",
 #' @param rt Numeric with the retention times for the spectra. If not provided
 #'     it is extracted from the spectra.
 #'
-#' @return a list of length 2, \code{peaks} containing a matrix with the
-#'     identified peaks and \code{date} the time stamp when the peak detection
+#' @return a list of length 2, `peaks` containing a matrix with the
+#'     identified peaks and `date` the time stamp when the peak detection
 #'     was started.
 #'
 #' @author Johannes Rainer
@@ -314,9 +314,9 @@ findPeaks_MSW_Spectrum_list <- function(x, method = "MSW", param) {
 
 #' @description Processes the result list returned by an lapply/bplapply to
 #'     findChromPeaks_Spectrum_list or findChromPeaks_OnDiskMSnExp and returns a
-#'     list with two elements: \code{$peaks} the peaks matrix of identified
-#'     peaks and \code{$procHist} a list of ProcessHistory objects (empty if
-#'     \code{getProcHist = FALSE}).
+#'     list with two elements: `$peaks` the peaks matrix of identified
+#'     peaks and `$procHist` a list of ProcessHistory objects (empty if
+#'     `getProcHist = FALSE`).
 #'
 #' @param x See description above.
 #'
@@ -363,14 +363,14 @@ findPeaks_MSW_Spectrum_list <- function(x, method = "MSW", param) {
 #' @note Adjustment should be performed only on spectra from the same MS level!
 #'     It's up to the calling function to ensure that.
 #'
-#' @param object An \code{OnDiskMSnExp}.
+#' @param object An `OnDiskMSnExp`.
 #'
-#' @param param An \code{ObiwarpParam}.
+#' @param param An `ObiwarpParam`.
 #'
-#' @param msLevel \code{integer} defining the MS level on which the adjustment
+#' @param msLevel `integer` defining the MS level on which the adjustment
 #'     should be performed.
 #'
-#' @return The function returns a \code{list} of adjusted retention times
+#' @return The function returns a `list` of adjusted retention times
 #'     grouped by file.
 #'
 #' @noRd

R/functions-Params.R

@@ -3,7 +3,7 @@
 
 ##
 #' @description Extract all slot values and put them into a list, names being
-#'     the slot names. If a slot \code{addParams} exist its content will be
+#'     the slot names. If a slot `addParams` exist its content will be
 #'     appended to the returned list.
 #'
 #' @param x A Param class.
@@ -66,22 +66,26 @@
 
 ############################################################
 ## GenericParam
-#' @return The \code{GenericParam} function returns a \code{GenericParam}
+#' @return The `GenericParam()` function returns a `GenericParam`
 #'     object.
 #'
-#' @param fun \code{character} representing the name of the function.
+#' @param fun `character` representing the name of the function.
 #'
-#' @param args \code{list} (ideally named) with the arguments to the function.
+#' @param args `list` (ideally named) with the arguments to the function.
+#'
+#' @md
 #'
 #' @rdname GenericParam
 GenericParam <- function(fun = character(), args = list()) {
     return(new("GenericParam", fun = fun, args = args))
 }
 
-#' @return The \code{CentWaveParam} function returns a \code{CentWaveParam}
+#' @return The `CentWaveParam()` function returns a `CentWaveParam`
 #'     class instance with all of the settings specified for chromatographic
 #'     peak detection by the centWave method.
 #'
+#' @md
+#'
 #' @rdname findChromPeaks-centWave
 CentWaveParam <- function(ppm = 25, peakwidth = c(20, 50), snthresh = 10,
                           prefilter = c(3, 100), mzCenterFun = "wMean",
@@ -99,11 +103,13 @@ CentWaveParam <- function(ppm = 25, peakwidth = c(20, 50), snthresh = 10,
                verboseBetaColumns=verboseBetaColumns))
 }
 
-#' @return The \code{MatchedFilterParam} function returns a
-#'     \code{MatchedFilterParam} class instance with all of the settings
-#'     specified for chromatographic detection by the \emph{matchedFilter}
+#' @return The `MatchedFilterParam()` function returns a
+#'     `MatchedFilterParam` class instance with all of the settings
+#'     specified for chromatographic detection by the *matchedFilter*
 #'     method.
 #'
+#' @md
+#'
 #' @rdname findChromPeaks-matchedFilter
 MatchedFilterParam <- function(binSize = 0.1, impute = "none",
                                baseValue = numeric(), distance = numeric(),
@@ -129,11 +135,13 @@ MatchedFilterParam <- function(binSize = 0.1, impute = "none",
     return("intlin")
 }
 
-#' @return The \code{MassifquantParam} function returns a
-#'     \code{MassifquantParam} class instance with all of the settings
-#'     specified for chromatographic peak detection by the \emph{massifquant}
+#' @return The `MassifquantParam()` function returns a
+#'     `MassifquantParam` class instance with all of the settings
+#'     specified for chromatographic peak detection by the *massifquant*
 #'     method.
 #'
+#' @md
+#'
 #' @rdname findChromPeaks-massifquant
 MassifquantParam <- function(ppm = 25, peakwidth = c(20, 50), snthresh = 10,
                              prefilter = c(3, 100), mzCenterFun = "wMean",
@@ -156,37 +164,39 @@ MassifquantParam <- function(ppm = 25, peakwidth = c(20, 50), snthresh = 10,
 #' @param scales Numeric defining the scales of the continuous wavelet
 #'     transform (CWT).
 #'
-#' @param nearbyPeak logical(1) whether to include nearby peaks of
+#' @param nearbyPeak `logical(1)` whether to include nearby peaks of
 #'     major peaks.
 #'
-#' @param peakScaleRange numeric(1) defining the scale range of the
+#' @param peakScaleRange `numeric(1)` defining the scale range of the
 #'     peak (larger than 5 by default).
 #'
-#' @param ampTh numeric(1) defining the minimum required relative
+#' @param ampTh `numeric(1)` defining the minimum required relative
 #'     amplitude of the peak (ratio of the maximum of CWT coefficients).
 #'
-#' @param minNoiseLevel numeric(1) defining the minimum noise level
+#' @param minNoiseLevel `numeric(1)` defining the minimum noise level
 #'     used in computing the SNR.
 #'
-#' @param ridgeLength numeric(1) defining the minimum highest scale
+#' @param ridgeLength `numeric(1)` defining the minimum highest scale
 #'     of the peak in 2-D CWT coefficient matrix.
 #'
-#' @param peakThr numeric(1) with the minimum absolute intensity
+#' @param peakThr `numeric(1)` with the minimum absolute intensity
 #'     (above baseline) of peaks to be picked. If provided, the smoothing
-#'     Savitzky-Golay filter is used (in the \code{MassSpecWavelet})
+#'     Savitzky-Golay filter is used (in the *MassSpecWavelet*)
 #'     package to estimate the local intensity.
 #'
-#' @param tuneIn logical(1) whther to tune in the parameter
+#' @param tuneIn `logical(1)` whther to tune in the parameter
 #'     estimation of the detected peaks.
 #'
 #' @param ... Additional parameters to be passed to the
-#'     \code{\link{peakDetectionCWT}} and
-#'     \code{\link{identifyMajorPeaks}} functions from the
-#'     \code{MassSpecWavelet} package.
+#'     `peakDetectionCWT()` and
+#'     `identifyMajorPeaks()` functions from the
+#'     *MassSpecWavelet* package.
 #'
-#' @return The \code{MSWParam} function returns a \code{MSWParam}
+#' @return The `MSWParam()` function returns a `MSWParam`
 #'     class instance with all of the settings specified for peak detection by
-#'     the \emph{MSW} method.
+#'     the *MSW* method.
+#'
+#' @md
 #'
 #' @rdname findPeaks-MSW
 MSWParam <- function(snthresh = 3, verboseColumns = FALSE,
@@ -205,11 +215,13 @@ MSWParam <- function(snthresh = 3, verboseColumns = FALSE,
                peakThr = peakThr, tuneIn = tuneIn, addParams = addParams))
 }
 
-#' @return The \code{CentWavePredIsoParam} function returns a
-#'     \code{CentWavePredIsoParam} class instance with all of the settings
+#' @return The `CentWavePredIsoParam()` function returns a
+#'     `CentWavePredIsoParam` class instance with all of the settings
 #'     specified for the two-step centWave-based peak detection considering also
 #'     isotopes.
 #'
+#' @md
+#'
 #' @rdname findChromPeaks-centWaveWithPredIsoROIs
 CentWavePredIsoParam <- function(ppm = 25, peakwidth = c(20, 50), snthresh = 10,
                           prefilter = c(3, 100), mzCenterFun = "wMean",
@@ -323,8 +335,10 @@ ObiwarpParam <- function(binSize = 1, centerSample = integer(), response = 1L,
         rtimeDifferenceThreshold = rtimeDifferenceThreshold[1L])
 }
 
-#' @return The \code{FillChromPeaksParam} function returns a
-#'     \code{FillChromPeaksParam} object.
+#' @return The `FillChromPeaksParam()` function returns a
+#'     `FillChromPeaksParam` object.
+#'
+#' @md
 #'
 #' @rdname fillChromPeaks
 FillChromPeaksParam <- function(expandMz = 0, expandRt = 0, ppm = 0,
@@ -339,7 +353,7 @@ fixedRt <- function(object) object@fixedRt
 #' @rdname fillChromPeaks
 fixedMz <- function(object) object@fixedMz
 
-#' @return The `CalibrantMassParam` function returns an instance of
+#' @return The `CalibrantMassParam()` function returns an instance of
 #'     the `CalibrantMassParam` class with all settings and properties set.
 #'
 #' @md

R/functions-XCMSnExp.R

@@ -140,26 +140,26 @@ dropGenericProcessHistory <- function(x, fun) {
 #'
 #' @note
 #'
-#' Ideally, \code{x} should be an \code{OnDiskMSnExp} object as subsetting
-#' of a \code{XCMSnExp} object is more costly (removing of preprocessing
+#' Ideally, `x` should be an `OnDiskMSnExp` object as subsetting
+#' of a `XCMSnExp` object is more costly (removing of preprocessing
 #' results, restoring data etc). If retention times reported in the
 #' featureData are replaced by adjusted retention times, these are set
 #' in the Spectrum objects as retention time.
 #'
-#' @param x An \code{OnDiskMSnExp} object.
+#' @param x An `OnDiskMSnExp` object.
 #'
-#' @param rt \code{numeric(2)} with the retention time range from which the
+#' @param rt `numeric(2)` with the retention time range from which the
 #'     data should be extracted.
 #'
-#' @param mz \code{numeric(2)} with the mz range.
+#' @param mz `numeric(2)` with the mz range.
 #'
-#' @param msLevel \code{integer} defining the MS level(s) to which the data
+#' @param msLevel `integer` defining the MS level(s) to which the data
 #'     should be restricted prior to data extraction.
 #'
 #' @return
 #'
-#' A \code{list} with length equal to the number of files and
-#' each element being a \code{data.frame} with the extracted values.
+#' A `list` with length equal to the number of files and
+#' each element being a `data.frame` with the extracted values.
 #'
 #' @noRd
 #'
@@ -212,23 +212,23 @@ dropGenericProcessHistory <- function(x, fun) {
 #'
 #' @note This reads the full data first and does the subsetting later in R.
 #'
-#' @param object An \code{XCMSnExp} object representing a single sample.
+#' @param object An `XCMSnExp` object representing a single sample.
 #'
-#' @param peakArea A \code{matrix} with the peak definition, i.e.
-#'     \code{"rtmin"}, \code{"rtmax"}, \code{"mzmin"} and \code{"mzmax"}.
+#' @param peakArea A `matrix` with the peak definition, i.e.
+#'     "rtmin", "rtmax", "mzmin" and "mzmax".
 #'
-#' @param sample_idx \code{integer(1)} with the index of the sample in the
+#' @param sample_idx integer(1) with the index of the sample in the
 #'     object.
 #'
 #' @param mzCenterFun Name of the function to be used to calculate the mz value.
-#'     Defaults to \code{weighted.mean}, i.e. the intensity weighted mean mz.
+#'     Defaults to weighted.mean, i.e. the intensity weighted mean mz.
 #'
-#' @param cn \code{character} with the names of the result matrix.
+#' @param cn character with the names of the result matrix.
 #'
 #' @return
 #'
-#' A \code{matrix} with at least columns \code{"mz"}, \code{"rt"},
-#' \code{"into"} and \code{"maxo"} with the by intensity weighted mean of
+#' A matrix with at least columns `"mz"`, `"rt"`,
+#' `"into"` and `"maxo"` with the by intensity weighted mean of
 #' mz, rt or the maximal intensity in the area, the integrated signal in
 #' the area and the maximal signal in the area.
 #'