Address William's comments

R/AllGenerics.R

@@ -541,20 +541,21 @@ setGeneric("chromPeakSpectra", function(object, ...)
 #'
 #' @description
 #'
-#' The `chromPeakSummary()` method calculates summary statistic or other
-#' metrics for each of the identified chromatographic peaks in an *xcms*
-#' result object, such as the [XcmsExperiment()]. Different metrics can be
-#' calculated, depending (and configured) using dedicated *parameter* classes.
-#' As a result, the method returns a `matrix` or `data.frame` with one row
-#' per chromatographic peak. Each column contains calculated values, depending
-#' on the used method/parameter class.
+#' The `chromPeakSummary()` method calculates summary statistics or other
+#' metrics for each of the identified chromatographic peaks in an *xcms* result
+#' object, such as the [XcmsExperiment()]. Different metrics can be calculated,
+#' depending upon (and configured by) using dedicated *parameter* classes. As a
+#' result, the method returns a `matrix` or `data.frame` with one row per
+#' chromatographic peak. Each column contains calculated values, depending on
+#' the used method/parameter class.
 #'
 #' Currently implemented methods/parameter classes are:
 #'
 #' - `BetaDistributionParam`: calculates the *beta_cor* and *beta_snr* quality
-#'   metrics as described in (Kumler 2023) representing the result from a
-#'   (correlation) test of similarity to a bell curve and the signal-to-noise
-#'   ratio calculated on the residulas of this test.
+#'   metrics as described in Kumler 2023 representing the result from a
+#'   (correlation) test of similarity (using Pearson's correlation coefficient)
+#'   to a bell curve and the signal-to-noise ratio calculated on the residuals
+#'   of this test.
 #'
 #' @param BPPARAM Parallel processing setup. See [bpparam()] for details.
 #'
@@ -579,7 +580,7 @@ setGeneric("chromPeakSpectra", function(object, ...)
 #' columns, their names and content depend on the used parameter object. See
 #' the respective documentation above for more details.
 #'
-#' @author Pablo Vangeenderhuysen, Johannes Rainer
+#' @author Pablo Vangeenderhuysen, Johannes Rainer, William Kumler
 #'
 #' @md
 #'

R/methods-XChromatogram.R

@@ -32,7 +32,7 @@ setMethod("show", "XChromatogram", function(object) {
 #'   value) and `"mzmax"` (maximal m/z value), `"rt"` (retention time of the
 #'   peak apex), `"rtmin"` (the lower peak boundary in retention time
 #'   dimension), `"rtmax"` (the upper peak boundary in retention time
-#'   dimension), `"into"` (the ingegrated peak signal/area of the peak),
+#'   dimension), `"into"` (the integrated peak signal/area of the peak),
 #'   `"maxo"` (the maximum instensity of the peak and `"sn"` (the signal to
 #'   noise ratio).
 #'   Note that, depending on the peak detection algorithm, the matrix may

vignettes/xcms.Rmd

@@ -470,7 +470,7 @@ eics <- chromPeakChromatograms(
     faahko, peaks = rownames(chromPeaks(faahko))[c(4, 6)])
 ```
 
-```{r peak-quality-metrics, fig.widht = 10, fig.height = 5, fig.cap = "Plots of high and low quality peaks. Left: peak CP0004 with a beta_cor = 0.98, right: peak CP0006 with a beta_cor = 0.13."}
+```{r peak-quality-metrics, fig.width = 10, fig.height = 5, fig.cap = "Plots of high and low quality peaks. Left: peak CP0004 with a beta_cor = 0.98, right: peak CP0006 with a beta_cor = 0.13."}
 peak_1 <- eics[1]
 peak_2 <- eics[2]
 par(mfrow = c(1, 2))
@@ -509,7 +509,7 @@ faahko_pp <- refineChromPeaks(faahko, mpp)
 
 An example for a merged peak is given below.
 
-```{r peak-postprocessing-merged, fig.widht = 10, fig.height = 5, fig.cap = "Result from the peak refinement step. Left: data before processing, right: after refinement. The splitted peak was merged into one."}
+```{r peak-postprocessing-merged, fig.width = 10, fig.height = 5, fig.cap = "Result from the peak refinement step. Left: data before processing, right: after refinement. The splitted peak was merged into one."}
 mzr_1 <- 305.1 + c(-0.01, 0.01)
 chr_1 <- chromatogram(faahko[1], mz = mzr_1)
 chr_2 <- chromatogram(faahko_pp[1], mz = mzr_1)
@@ -524,7 +524,7 @@ plot(chr_2)
 peaks into a single one (right panel in the figure above). Other close peaks,
 with a lower intensity between them, were however not merged (see below).
 
-```{r peak-postprocessing-not-merged, fig.widht = 10, fig.height = 5, fig.cap = "Result from the peak refinement step. Left: data before processing, right: after refinement. The peaks were not merged."}
+```{r peak-postprocessing-not-merged, fig.width = 10, fig.height = 5, fig.cap = "Result from the peak refinement step. Left: data before processing, right: after refinement. The peaks were not merged."}
 mzr_1 <- 496.2 + c(-0.01, 0.01)
 chr_1 <- chromatogram(faahko[1], mz = mzr_1)
 chr_2 <- chromatogram(faahko_pp[1], mz = mzr_1)