fix: fix issue #302

- Allow optional parameters (...) to avoid errors if `filterFourierTransformArtefacts` is combined with another peaks function.
rformassspectrometry · Sep 25, 2023 · 6d16816 · 6d16816
1 parent 585abb1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.11.10
+Version: 1.11.11
 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

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,11 @@
 # Spectra 1.11
 
+## Changes in 1.11.11
+
+- Fix issue with `filterFourierTransformArtefacts` function (see [issue
+  #302](https://github.com/rformassspectrometry/Spectra/issues/302)). Thanks
+  Adriano Rutz for reporting.
+
 ## Changes in 1.11.10
 
 - `peaksData,MsBackendMemory` returns a `data.frame` if additional peak

diff --git a/R/peaks-functions.R b/R/peaks-functions.R
@@ -480,7 +480,7 @@ joinPeaksNone <- function(x, y, ...) {
                                        threshold = 0.2,
                                        keepIsotopes = TRUE,
                                        maxCharge = 5,
-                                       isotopeTolerance = 0.005) {
+                                       isotopeTolerance = 0.005, ...) {
     neutron   <- 1.0033548378 # really C12, C13 difference
     iso_dist  <- neutron / seq(from = 1, by = 1, to = maxCharge)
     ## just calculate isotopes that are in the halfWindowSize
@@ -638,7 +638,7 @@ joinPeaksNone <- function(x, y, ...) {
 #' @noRd
 .peaks_filter_precursor_ne <- function(x, ppm = 20, tolerance = 0,
                                        precursorMz, spectrumMsLevel,
-                                       msLevel = spectrumMsLevel) {
+                                       msLevel = spectrumMsLevel, ...) {
     if (!spectrumMsLevel %in% msLevel || !nrow(x))
         return(x)
     keep <- is.na(closest(x[, "mz"], precursorMz, ppm = ppm,
@@ -656,7 +656,7 @@ joinPeaksNone <- function(x, y, ...) {
 #' @noRd
 .peaks_filter_precursor_keep_below <- function(x, ppm = 20, tolerance = 0,
                                                precursorMz, spectrumMsLevel,
-                                               msLevel = spectrumMsLevel) {
+                                               msLevel = spectrumMsLevel, ...) {
     if (!spectrumMsLevel %in% msLevel || !nrow(x))
         return(x)
     pmz <- precursorMz - tolerance - ppm(precursorMz, ppm = ppm)