refactor: cleanup NAMESPACE and dependencies and documentation

- Re-save data object. - Fix documentation and unit tests following the move of `MSnbase` from Depends to Imports.
sneumann · Mar 14, 2024 · 086999d · 086999d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.1.10
+Version: 4.1.11
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,
@@ -82,14 +82,14 @@ Suggests:
     signal
 Enhances:
     Rgraphviz,
-    rgl,
-    XML
+    rgl
 License: GPL (>= 2) + file LICENSE
 URL: https://github.com/sneumann/xcms
 BugReports: https://github.com/sneumann/xcms/issues/new
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, MassSpectrometry, Metabolomics
 RoxygenNote: 7.3.1
+Encoding: UTF-8
 Collate:
     'AllGenerics.R'
     'functions-XChromatograms.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -581,6 +581,8 @@ importFrom("progress", "progress_bar")
 exportClasses("XcmsExperiment")
 exportMethods("uniqueMsLevels")
 exportMethods("filterMzRange")
+exportMethods("fromFile")
+exportMethods("fileNames")
 
 ## saving xcms objects things
 importFrom("jsonlite", "serializeJSON", "write_json", "unserializeJSON",

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -321,6 +321,9 @@ setGeneric("checkBack<-", function(object, value) standardGeneric("checkBack<-")
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
+#' library(xcms)
+#' library(MsExperiment)
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
 #' ## Get EICs for every detected chromatographic peak
@@ -698,6 +701,8 @@ setGeneric("family<-", function(object, value) standardGeneric("family<-"))
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(xcms)
+#' library(MsExperiment)
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
 #' ## Disable parallel processing for this example
@@ -999,14 +1004,16 @@ setGeneric("filepaths<-", function(object, value) standardGeneric("filepaths<-")
 #' @examples
 #'
 #' ## Load a test data set with identified chromatographic peaks
+#' library(xcms)
+#' library(MsExperiment)
 #' res <- loadXcmsData("faahko_sub2")
 #'
 #' ## Disable parallel processing for this example
 #' register(SerialParam())
 #'
 #' ## Perform the correspondence. We assign all samples to the same group.
 #' res <- groupChromPeaks(res,
-#'     param = PeakDensityParam(sampleGroups = rep(1, length(fileNames(res)))))
+#'     param = PeakDensityParam(sampleGroups = rep(1, length(res))))
 #'
 #' ## For how many features do we lack an integrated peak signal?
 #' sum(is.na(featureValues(res)))
@@ -1897,6 +1904,8 @@ setGeneric("reconstructChromPeakSpectra", function(object, ...)
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(xcms)
+#' library(MsExperiment)
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
 #' ## Disable parallel processing for this example
@@ -2047,6 +2056,8 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(xcms)
+#' library(MsExperiment)
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
 #' ## Set up parameter to save as .RData file

diff --git a/R/DataClasses.R b/R/DataClasses.R
@@ -489,7 +489,7 @@ setClass("XProcessHistory",
 #' detection in purely chromatographic data.
 #'
 #' @references
-#' Ralf Tautenhahn, Christoph B\"{o}ttcher, and Steffen Neumann "Highly
+#' Ralf Tautenhahn, Christoph Böttcher, and Steffen Neumann "Highly
 #' sensitive feature detection for high resolution LC/MS" \emph{BMC Bioinformatics}
 #' 2008, 9:504
 #'
@@ -519,13 +519,14 @@ NULL
 #' cwp
 #'
 #' ## Perform the peak detection using centWave on some of the files from the
-#' ## faahKO package. Files are read using the readMSData from the MSnbase
-#' ## package
+#' ## faahKO package. Files are read using the `readMsExperiment` function
+#' ## from the MsExperiment package
 #' library(faahKO)
 #' library(xcms)
+#' library(MsExperiment)
 #' fls <- dir(system.file("cdf/KO", package = "faahKO"), recursive = TRUE,
 #'            full.names = TRUE)
-#' raw_data <- readMSData(fls[1], mode = "onDisk")
+#' raw_data <- readMsExperiment(fls[1])
 #'
 #' ## Perform the peak detection using the settings defined above.
 #' res <- findChromPeaks(raw_data, param = cwp)
@@ -894,7 +895,7 @@ setClass("MatchedFilterParam",
 #'     centWave algorithm, which includes wavelet estimation.
 #'
 #' @details This algorithm's performance has been tested rigorously
-#'     on high resolution LC/{OrbiTrap, TOF}-MS data in centroid mode.
+#'     on high resolution LC/(OrbiTrap, TOF)-MS data in centroid mode.
 #'     Simultaneous kalman filters identify chromatographic peaks and calculate
 #'     their area under the curve. The default parameters are set to operate on
 #'     a complex LC-MS Orbitrap sample. Users will find it useful to do some
@@ -1110,6 +1111,7 @@ NULL
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' ## Create a MSWParam object
 #' mp <- MSWParam()
 #' ## Change snthresh parameter
@@ -1799,6 +1801,7 @@ setClass("MsFeatureData", contains = c("environment"),
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")

diff --git a/R/do_findChromPeaks-functions.R b/R/do_findChromPeaks-functions.R
@@ -68,7 +68,8 @@
 #' @family core peak detection functions
 #'
 #' @references
-#' Ralf Tautenhahn, Christoph B\"{o}ttcher, and Steffen Neumann "Highly
+#'
+#' Ralf Tautenhahn, Christoph Böttcher, and Steffen Neumann "Highly
 #'     sensitive feature detection for high resolution LC/MS"
 #'     \emph{BMC Bioinformatics} 2008, 9:504
 #'
@@ -163,7 +164,7 @@ do_findChromPeaks_centWave <- function(mz, int, scantime, valsPerSpect,
                        verboseColumns = verboseColumns, roiList = roiList,
                        firstBaselineCheck = firstBaselineCheck,
                        roiScales = roiScales, sleep = sleep,
-                       extendLengthMSW = extendLengthMSW, 
+                       extendLengthMSW = extendLengthMSW,
                        verboseBetaColumns = verboseBetaColumns)
     } else {
         ## message("DEBUG: using modified centWave.")
@@ -579,7 +580,7 @@ do_findChromPeaks_centWave <- function(mz, int, scantime, valsPerSpect,
                 lm <- .narrow_rt_boundaries(lm, d)
                 lm_seq <- lm[1]:lm[2]
                 pd <- d[lm_seq]
-                
+
                 # Implement a fit of a skewed gaussian (beta distribution)
                 # for peak shape and within-peak signal-to-noise ratio
                 # See https://doi.org/10.1186/s12859-023-05533-4 and
@@ -1265,7 +1266,7 @@ do_findChromPeaks_centWave <- function(mz, int, scantime, valsPerSpect,
 #'     by specifying \code{withWave = TRUE}.
 #'
 #' @details This algorithm's performance has been tested rigorously
-#'     on high resolution LC/{OrbiTrap, TOF}-MS data in centroid mode.
+#'     on high resolution LC/(OrbiTrap, TOF)-MS data in centroid mode.
 #'     Simultaneous kalman filters identify peaks and calculate their
 #'     area under the curve. The default parameters are set to operate on
 #'     a complex LC-MS Orbitrap sample. Users will find it useful to do some
@@ -2673,7 +2674,7 @@ do_findChromPeaks_centWaveWithPredIsoROIs <-
              verboseColumns = FALSE, roiList = list(),
              firstBaselineCheck = TRUE, roiScales = NULL, snthreshIsoROIs = 6.25,
              maxCharge = 3, maxIso = 5, mzIntervalExtension = TRUE,
-             polarity = "unknown", extendLengthMSW = FALSE, 
+             polarity = "unknown", extendLengthMSW = FALSE,
              verboseBetaColumns = FALSE) {
         ## Input argument checking: most of it will be done in
         ## do_findChromPeaks_centWave
@@ -3271,9 +3272,9 @@ peaksWithMatchedFilter <- function(int, rt, fwhm = 30, sigma = fwhm / 2.3548,
 #' @examples
 #'
 #' ## Reading a file
+#' library(MsExperiment)
 #' library(xcms)
-#' od <- readMSData(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
-#'     mode = "onDisk")
+#' od <- readMsExperiment(system.file("cdf/KO/ko15.CDF", package = "faahKO"))
 #'
 #' ## Extract chromatographic data for a small m/z range
 #' mzr <- c(272.1, 272.2)
@@ -3633,9 +3634,9 @@ peaksWithCentWave <- function(int, rt,
 #'
 #' @examples
 #'
+#' library(MsExperiment)
 #' library(xcms)
-#' od <- readMSData(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
-#'     mode = "onDisk")
+#' od <- readMsExperiment(system.file("cdf/KO/ko15.CDF", package = "faahKO"))
 #'
 #' ## Extract chromatographic data for a small m/z range
 #' chr <- chromatogram(od, mz = c(272.1, 272.3))[1, 1]
@@ -3731,7 +3732,7 @@ peaksWithCentWave <- function(int, rt,
 #' @author William Kumler
 #'
 #' @noRd
-.get_beta_values <- function(intensity, rtime = seq_along(intensity), 
+.get_beta_values <- function(intensity, rtime = seq_along(intensity),
                              skews=c(3, 3.5, 4, 4.5, 5), zero.rm = TRUE){
   if (zero.rm) {
     ## remove 0 or NA intensities
@@ -3744,7 +3745,7 @@ peaksWithCentWave <- function(int, rt,
     beta_snr <- NA
   } else {
     beta_sequence <- rep(.scale_zero_one(rtime), each=length(skews))
-    beta_vals <- t(matrix(dbeta(beta_sequence, shape1 = skews, shape2 = 5), 
+    beta_vals <- t(matrix(dbeta(beta_sequence, shape1 = skews, shape2 = 5),
                           nrow = length(skews)))
     # matplot(beta_vals)
     beta_cors <- cor(intensity, beta_vals)

diff --git a/R/do_groupChromPeaks-functions.R b/R/do_groupChromPeaks-functions.R
@@ -75,6 +75,8 @@
 #'
 #' @examples
 #' ## Load the test file
+#' library(xcms)
+#' library(MsExperiment)
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #'
 #' ## Disable parallel processing for this example

diff --git a/R/functions-Chromatogram.R b/R/functions-Chromatogram.R
@@ -62,8 +62,8 @@
 #'
 #' @examples
 #'
-#' xd <- readMSData(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
-#'     mode = "onDisk")
+#' library(MsExperiment)
+#' xd <- readMsExperiment(system.file('cdf/KO/ko15.CDF', package = "faahKO"))
 #' chr <- chromatogram(xd, mz = c(-0.5, 0.5) + 453.2)
 #' xchr <- findChromPeaks(chr, param = CentWaveParam(snthresh = 0))
 #' plot(xchr)

diff --git a/R/functions-OnDiskMSnExp.R b/R/functions-OnDiskMSnExp.R
@@ -703,6 +703,7 @@ setReplaceMethod("dirname", "OnDiskMSnExp", function(path, value) {
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
 #' pest_dda <- readMSData(fl, mode = "onDisk")
 #' res <- .estimate_prec_intensity(pest_dda)

diff --git a/R/functions-XCMSnExp.R b/R/functions-XCMSnExp.R
@@ -796,6 +796,7 @@ adjustRtimePeakGroups <- function(object, param = PeakGroupsParam(),
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
@@ -964,6 +965,7 @@ isCalibrated <- function(object) {
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
@@ -1202,6 +1204,7 @@ featureSummary <- function(x, group, perSampleCounts = FALSE,
 #' @examples
 #'
 #' ## Load a test data set with detected peaks
+#' library(MSnbase)
 #' data(faahko_sub)
 #' ## Update the path to the files for the local system
 #' dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
@@ -1854,6 +1857,7 @@ setMethod("hasFilledChromPeaks", "XCMSnExp", function(object) {
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' xd <- readMSData(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
 #'     mode = "onDisk")
 #' xd <- findChromPeaks(xd, param = CentWaveParam())

diff --git a/R/functions-XChromatogram.R b/R/functions-XChromatogram.R
@@ -141,6 +141,7 @@
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' ## Create a XChromatogram object
 #' pks <- matrix(nrow = 1, ncol = 6)
 #' colnames(pks) <- c("rt", "rtmin", "rtmax", "into", "maxo", "sn")

diff --git a/R/functions-XChromatograms.R b/R/functions-XChromatograms.R
@@ -43,6 +43,7 @@
 #' ## ---- Creation of XChromatograms ----
 #' ##
 #' ## Create a XChromatograms from Chromatogram objects
+#' library(MSnbase)
 #' dta <- list(Chromatogram(rtime = 1:7, c(3, 4, 6, 12, 8, 3, 2)),
 #'     Chromatogram(1:10, c(4, 6, 3, 4, 7, 13, 43, 34, 23, 9)))
 #'

diff --git a/R/functions-imputation.R b/R/functions-imputation.R
@@ -22,6 +22,7 @@
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' library(faahKO)
 #' data("faahko")
 #'
@@ -111,6 +112,7 @@ imputeRowMin <- function(x, min_fraction = 1/2) {
 #' @examples
 #'
 #' library(faahKO)
+#' library(MSnbase)
 #' data("faahko")
 #'
 #' xset <- group(faahko)

diff --git a/R/functions-utils.R b/R/functions-utils.R
@@ -307,8 +307,9 @@ weightedMeanAroundApex <- function(x, w = rep(1, length(x)), i = 1) {
 #'
 #' @description
 #'
-#' **UPDATE**: please use `plot(x, type = "XIC")` from the `MSnbase` package
-#' instead. See examples below.
+#' **UPDATE**: please use `plot()` from the `MsExperiment` or
+#' `plot(x, type = "XIC")` from the `MSnbase` package instead. See examples
+#' in the vignette for more information.
 #'
 #' The `plotMsData` creates a plot that combines an (base peak )
 #' extracted ion chromatogram on top (rt against intensity) and a plot of
@@ -338,19 +339,6 @@ weightedMeanAroundApex <- function(x, w = rep(1, length(x)), i = 1) {
 #'
 #' @md
 #'
-#' @examples
-#'
-#' ## Read two files from the faahKO package
-#' library(faahKO)
-#' cdfs <- dir(system.file("cdf", package = "faahKO"), full.names = TRUE,
-#'     recursive = TRUE)[1:2]
-#' raw_data <- readMSData(cdfs, mode = "onDisk")
-#'
-#' ## Subset the object to a rt and mz range and plot the data.
-#' raw_data |>
-#'     filterRt(rt = c(2700, 2900)) |>
-#'     filterMz(mz = c(334.9, 335.1)) |>
-#'     plot(type = "XIC")
 plotMsData <- function(x, main = "", cex = 1, mfrow = c(2, 1),
                        grid.color = "lightgrey",
                        colramp = colorRampPalette(

diff --git a/R/methods-Chromatogram.R b/R/methods-Chromatogram.R
@@ -45,6 +45,7 @@
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' ## Loading a test data set with identified chromatographic peaks
 #' faahko_sub <- loadXcmsData("faahko_sub2")
 #' faahko_sub <- filterRt(faahko_sub, c(2500, 3700))
@@ -192,6 +193,7 @@ setMethod("findChromPeaks", signature(object = "Chromatogram",
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' chr1 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
 #'     intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))
 #' chr2 <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
@@ -261,6 +263,7 @@ setMethod("correlate", signature = c(x = "Chromatogram", y = "Chromatogram"),
 #'
 #' @examples
 #'
+#' library(MSnbase)
 #' chr <- Chromatogram(rtime = 1:10 + rnorm(n = 10, sd = 0.3),
 #'     intensity = c(5, 29, 50, NA, 100, 12, 3, 4, 1, 3))
 #'