docs: fix Phili's comments

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.15.4
+Version: 1.15.5
 Description: The Spectra package defines an efficient infrastructure
    for storing and handling mass spectrometry spectra and functionality to
    subset, process, visualize and compare spectra data. It provides different

R/MsBackend.R

@@ -774,7 +774,7 @@
 #'
 #' @return See documentation of respective function.
 #'
-#' @author Johannes Rainer, Sebastian Gibb, Laurent Gatto
+#' @author Johannes Rainer, Sebastian Gibb, Laurent Gatto, Philippine Louail
 #'
 #' @md
 #'

R/Spectra-functions.R

@@ -1194,11 +1194,11 @@ processingChunkFactor <- function(x) {
 #' has to be an available spectra or peaks variable. `<range>` can be a
 #' `numeric` of length 2 defining the lower and upper boundary, or a `numeric`
 #' two-column matrix (multi-row matrices are also supported, see further
-#' below). `filterPeaksRanges(s, mz = c(200, 300))` woudl for example reduce
+#' below). `filterPeaksRanges(s, mz = c(200, 300))` would for example reduce
 #' the peaks matrices of the `Spectra` object `s` to mass peaks with an m/z
 #' value between 200 and 300. `filterPeaksRanges()` returns the original
 #' `Spectra` object with the filter operation added to the processing queue.
-#' Thus, the filter gets only applied when the peaks data gets extracted
+#' Thus, the filter gets **only** applied when the peaks data gets extracted
 #' with `mz()`, `intensity()` or `peaksData()`. If ranges for both spectra
 #' **and** peaks variables are defined, the function evaluates first whether
 #' the spectra variable value for a spectrum is within the provided range and,
@@ -1221,19 +1221,24 @@ processingChunkFactor <- function(x) {
 #' or peaks variables) have to match.
 #'
 #' **Missing value handling**: any comparison which involves a missing value
-#' (beingvit a spectra variable value, a peaks variable value or a value
-#' in one of thevprovided ranges) is treated as a logical `FALSE`. For
+#' (being it a spectra variable value, a peaks variable value or a value
+#' in one of the provided ranges) is treated as a logical `FALSE`. For
 #' example, if the retention time of a spectrum is `NA` and the data is
 #' filtered using a retention time range, an empty peaks matrix is returned
 #' (for `keep = TRUE`, for `keep = FALSE` the full peaks matrix is returned).
 #'
 #' @note
 #'
-#' In contrast to other *filter* functions, this function does not provide a
-#' `msLevel.` parameter to apply the filter only on spectra of the specified
-#' MS levels. In contrast, to apply no, or different, filters to spectra from
-#' different MS levels, multi-row range matrices can be used (see examples
-#' below).
+#' In contrast to some other *filter* functions, this function does not provide
+#' a `msLevel` parameter that allows to define the MS level of spectra on which
+#' the filter should be applied. The filter(s) will always be applied to
+#' **all** spectra (irrespectively of their MS level). Through combination of
+#' multiple filter ranges it is however possible to apply MS level-dependent
+#' filters (see examples below for details).
+#'
+#' The filter will not be applied immediately to the data but only executed when
+#' the mass peak data is accessed (through `peaksData()`, `mz()` or
+#' `intensity()`) or by calling `applyProcessing()`.
 #'
 #' @param object A [Spectra] object.
 #'

R/Spectra.R

@@ -334,10 +334,10 @@ NULL
 #' @section Filter spectra data:
 #'
 #' Filter a `Spectra` object based on the spectra data. This includes subset
-#' operations that reduce the number of spectra in the object as well as filters
-#' that reduce the *content* of the `Spectra` object. See section
-#' *Filter peaks data* below for functions that filter the peaks data of a
-#' `Spectra`.
+#' operations that immediately reduce the number of spectra in the object as
+#' well as filters that reduce the *content* of the `Spectra` object.
+#' See section *Filter peaks data* below for functions that filter the peaks
+#' data of a `Spectra`.
 #'
 #' - `[`: subsets the spectra keeping only selected elements (`i`). The method
 #'   **always** returns a `Spectra` object.
@@ -456,7 +456,10 @@ NULL
 #' @section Filter or aggregate mass peak data:
 #'
 #' Operations that filter or aggregate the mass peak data from each spectrum
-#' without changing the number of spectra in a `Spectra` object.
+#' without changing the number of spectra in a `Spectra` object. Also, the
+#' actual subsetting/aggregation operation is only executed once peaks data is
+#' accessed (through `peaksData()`, `mz()` or `intensity()`) or
+#' `applyProcessing()` is called.
 #'
 #' - `combinePeaks()`: combines mass peaks **within each spectrum** with a
 #'   difference in their m/z values that is smaller than the maximal
@@ -1115,7 +1118,7 @@ NULL
 #'
 #' @param ... Additional arguments.
 #'
-#' @author Sebastian Gibb, Johannes Rainer, Laurent Gatto
+#' @author Sebastian Gibb, Johannes Rainer, Laurent Gatto, Philippine Louail
 #'
 #' @md
 #'