refactor: calculate beta columns for gap filling of XcmsExperiment

- Bump version.
- Calculate beta peak shape quality metrics also during gap filling for
  `XcmsExperiment` objects.
- Add related unit tests.

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.1.2
+Version: 4.1.3
 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,
@@ -30,7 +30,7 @@ Authors@R: c(
  email = "[email protected]",
  role = "ctb"),
  person(given = "William", family = "Kumler",
- email = "[email protected]", role = "ctb",
+ email = "[email protected]", role = "aut",
  comment = c(ORCID = "0000-0002-5022-8009")),
  person(given = "Philippine", family = "Louail",
  email = "[email protected]",
@@ -70,7 +70,7 @@ Suggests:
  faahKO,
  msdata (>= 0.25.1),
  ncdf4,
- testthat,
+ testthat (>= 3.1.9),
  pander,
  rmarkdown,
  MALDIquant,

R/XcmsExperiment-functions.R

@@ -519,6 +519,9 @@
  sum(mat[, 2L], na.rm = TRUE) *
  ((rtr[2L] - rtr[1L]) / max(1L, (length(keep) - 1L)))
  )
+ if ("beta_cor" %in% cn)
+ res[i, c("beta_cor", "beta_snr")] <- .get_beta_values(
+ mat[, 2L], rts)
  }
  }
  }

R/functions-XCMSnExp.R

@@ -300,9 +300,10 @@ dropGenericProcessHistory <- function(x, fun) {
  meanMz <- do.call(mzCenterFun, list(mtx[, 2], mtx[, 3]))
  if (is.na(meanMz)) meanMz <- mtx[maxi[1], 2]
  res[i, "mz"] <- meanMz
-
- if("beta_cor"%in%cn){
- res[i, c("beta_cor", "beta_snr")] <- .get_beta_values(mtx[,3])
+
+ if ("beta_cor" %in% cn) {
+ res[i, c("beta_cor", "beta_snr")] <- .get_beta_values(
+ mtx[, 3L], mtx[, 1L])
  }
  } else {
  res[i, ] <- rep(NA_real_, ncols)

R/methods-XCMSnExp.R

@@ -1460,6 +1460,8 @@ setMethod("smooth", "XCMSnExp", function(x, method = c("SavitzkyGolay",
 setAs(from = "XCMSnExp", to = "xcmsSet", def = .XCMSnExp2xcmsSet)
 
 #' @rdname XcmsExperiment
+#'
+#' @name XcmsExperiment
 setAs(from = "XcmsExperiment", to = "xcmsSet", def = .XCMSnExp2xcmsSet)
 
 #' @rdname XCMSnExp-peak-grouping-results

inst/NEWS

@@ -1,3 +1,10 @@
+Changes in version 4.1.3
+----------------------
+
+- Add parameter `verboseBetaColumns` to `CentWaveParam` to enable calculation
+ of additional peak quality metrics comparing the EIC to an idealized bell
+ curve.
+
 Changes in version 4.1.2
 ----------------------
 

tests/testthat/test_XcmsExperiment.R

@@ -1326,3 +1326,16 @@ test_that("storeResults,RDataParam works", {
  expect_s4_class(object, "XcmsExperiment")
  expect_equal(object, xmse)
 })
+
+test_that("fillChromPeaks,XcmsExperiment works with verboseBetaColumns", {
+ p <- CentWaveParam(noise = 10000, snthresh = 40, prefilter = c(3, 10000),
+ verboseBetaColumns = TRUE)
+ res <- findChromPeaks(mse, param = p)
+ expect_true(all(c("beta_cor", "beta_snr") %in% colnames(chromPeaks(res))))
+ p <- PeakDensityParam(sampleGroups = rep(1, 3))
+ res <- groupChromPeaks(res, param = p)
+ res <- fillChromPeaks(res, ChromPeakAreaParam())
+ pks_det <- chromPeaks(res)[!chromPeakData(res)$is_filled, ]
+ pks_fil <- chromPeaks(res)[chromPeakData(res)$is_filled, ]
+ expect_true(!any(is.na(pks_fil[, "beta_cor"])))
+})