refactor: import breaks_ppm from MsCoreUtils

- Import `breaks_ppm` from `MsCoreUtils`.
- Update documentation.

DESCRIPTION

@@ -56,9 +56,9 @@ Imports:
     robustbase,
     IRanges,
     SummarizedExperiment,
-    MsCoreUtils (>= 1.11.5),
+    MsCoreUtils (>= 1.15.3),
     MsFeatures,
-    MsExperiment (>= 1.1.2),
+    MsExperiment (>= 1.5.3),
     Spectra (>= 1.13.2),
     progress,
     multtest,
@@ -87,7 +87,7 @@ URL: https://github.com/sneumann/xcms
 BugReports: https://github.com/sneumann/xcms/issues/new
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, MassSpectrometry, Metabolomics
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Collate:
     'AllGenerics.R'
     'functions-XChromatograms.R'

NAMESPACE

@@ -36,7 +36,7 @@ importMethodsFrom("S4Vectors", "as.matrix", "mcols", "mcols<-",
                   "extractROWS", "findMatches")
 importFrom("SummarizedExperiment", "SummarizedExperiment")
 importFrom("MsCoreUtils", "rbindFill", "closest", "i2index", "sumi", "between",
-           "maxi")
+           "maxi", "breaks_ppm")
 
 ## Additional imports proposed by R CMD check:
 importFrom("graphics", "abline", "barplot", "close.screen", "hist",
@@ -593,4 +593,3 @@ importFrom("jsonlite", "serializeJSON", "write_json", "unserializeJSON",
 export("RDataParam")
 export("PlainTextParam")
 exportMethods("storeResults")
-

R/do_groupChromPeaks-functions.R

@@ -132,7 +132,7 @@ do_groupChromPeaks_density <- function(peaks, sampleGroups,
     ## Define the mass slices and the index in the peaks matrix with an mz
     ## value >= mass[i]. If ppm != 0 the size of the individual bins will
     ## be dependend on the m/z value.
-    mass <- .breaks_ppm(peaks[1, "mz"], peaks[nrow(peaks), "mz"] + binSize,
+    mass <- breaks_ppm(peaks[1, "mz"], peaks[nrow(peaks), "mz"] + binSize,
                        by = binSize / 2, ppm = ppm / 2)
     masspos <- findEqualGreaterM(peaks[, "mz"], mass)
 
@@ -562,23 +562,3 @@ do_groupChromPeaks_nearest <- function(peaks, sampleGroups, mzVsRtBalance = 10,
     }
     x
 }
-
-#' Generate a sequence of values with increasing difference between consecutive
-#' values. The difference is increased using the `ppm`.
-#'
-#' Add that also to MsCoreUtils and eventually replace
-#'
-#' @noRd
-.breaks_ppm <- function(from = 1, to = 1, by = 1, ppm = 0) {
-    l <- ceiling((to - from + 1) / by)
-    res <- rep(NA_real_, l)
-    res[1L] <- a <- from
-    i <- 2L
-    while(a < to) {
-        a <- a + by
-        a <- a + (a * ppm * 1e-6)
-        res[i] <- a
-        i <- i + 1L
-    }
-    res[!is.na(res)]
-}

inst/NEWS

@@ -1,6 +1,8 @@
 Changes in version 4.1.6
 ----------------------
 
+- Import `filterSpectra` from `MsExperiment`.
+- Import `breaks_ppm` from `MsCoreUtils`.
 - Update `featureArea` function to consider all chromatographic peaks per
   feature, not only the one with the highest intensity. As a consequence,
   returned m/z and rt ranges might be higher which has an influence in