Additional preprocessing of noisy spectra

Adafede · Adafede · commit 11e80113aa4e · 2024-06-01T13:26:16.000+02:00
diff --git a/NEWS.md b/NEWS.md
@@ -5,6 +5,7 @@
 * Automated update
 * Added an option to remove ties (#134)
 * Added some details for SIRIUS, add manual workspace addition (#132)
+* Additional preprocessing (reduction) of noisy spectra
 * Docker updates (#131)
 * Handle cases when same (feature_id, mslevel) pairs are present within an MGF (#133)
 * Improved documentation
diff --git a/R/cleanup_spectra.R b/R/cleanup_spectra.R
@@ -10,6 +10,8 @@
 #'
 #' @examples NULL
 cleanup_spectra <- function(spectra) {
+  spectra <- spectra |>
+    Spectra::reduceSpectra()
   if ("MSLEVEL" %in% colnames(spectra@backend@spectraData)) {
     spectra <- spectra[spectra$MSLEVEL == 2]
   }

Original file line number	Diff line number	Diff line change
`@@ -10,6 +10,8 @@`
`10`	`10`	`#'`
`11`	`11`	`#' @examples NULL`
`12`	`12`	`cleanup_spectra <- function(spectra) {`
	`13`	`+ spectra <- spectra \|>`
	`14`	`+ Spectra::reduceSpectra()`
`13`	`15`	`if ("MSLEVEL" %in% colnames(spectra@backend@spectraData)) {`
`14`	`16`	`spectra <- spectra[spectra$MSLEVEL == 2]`
`15`	`17`	`}`