Merge pull request #309 from mar-garcia/main

add entropy functions

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Spectra
 Title: Spectra Infrastructure for Mass Spectrometry Data
-Version: 1.13.3
+Version: 1.13.4
 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
@@ -32,6 +32,10 @@ Authors@R: c(person(given = "RforMassSpectrometry Package Maintainer",
                     comment = c(ORCID = "0000-0003-0541-7369")),
              person(given = "Nir", family = "Shahaf",
                     email = "[email protected]",
+                    role = "ctb"),
+             person(given = "Mar", family = "Garcia-Aloy",
+                    email = "[email protected]",
+                    comment = c(ORCID = "0000-0002-1330-6610"),
                     role = "ctb"))
 Depends:
     R (>= 4.0.0),

NEWS.md

@@ -1,5 +1,10 @@
 # Spectra 1.13
 
+## Changes in 1.13.4
+
+- Add `entropy` and `nentropy` functions to allow to calculate the (normalized) 
+  entropy for each spectrum.
+
 ## Changes in 1.13.3
 
 - Fix issue in `setBackend` that might cause chunk-wise processing to be not

R/AllGenerics.R

@@ -27,6 +27,9 @@ setGeneric("containsNeutralLoss", function(object, ...)
 setGeneric("dropNaSpectraVariables", function(object, ...)
     standardGeneric("dropNaSpectraVariables"))
 #' @rdname hidden_aliases
+setGeneric("entropy", function(object, ...)
+  standardGeneric("entropy"))
+#' @rdname hidden_aliases
 setGeneric("export", function(object, ...)
     standardGeneric("export"))
 setGeneric("filterFourierTransformArtefacts", function(object, ...)

R/Spectra.R

@@ -659,6 +659,9 @@ NULL
 #'   documentation of [isotopologues()] for more information. The approach
 #'   and code to define the parameters for isotope prediction is described
 #'   [here](https://github.com/EuracBiomedicalResearch/isotopologues).
+#'   
+#' - `entropy`: calculates the entropy of each spectra based on the metrics suggested by 
+#'    Li et al. (https://doi.org/10.1038/s41592-021-01331-z).
 #'
 #' - `estimatePrecursorIntensity`: defines the precursor intensities for MS2
 #'   spectra using the intensity of the matching MS1 peak from the
@@ -2639,3 +2642,17 @@ setMethod("combinePeaks", "Spectra", function(object, tolerance = 0, ppm = 20,
         ppm, " and tolerance = ", tolerance, ".")
     object
 })
+
+
+#' @rdname Spectra
+#'
+#' @importFrom MsCoreUtils entropy nentropy
+setMethod("entropy", "Spectra", function(object, normalized = TRUE) {
+  if (normalized) entropy_fun <- nentropy
+  else entropy_fun <- entropy
+  unlist(.peaksapply(
+    object, FUN = function(pks, ...) entropy_fun(pks[, "intensity"])), 
+    use.names = FALSE
+  )
+})
+

tests/testthat/test_Spectra.R

@@ -1783,3 +1783,21 @@ test_that("processingChunkSize works", {
     processingChunkSize(tmp) <- 10
     expect_equal(processingChunkSize(tmp), 10)
 })
+
+test_that("entropy,Spectra works", {
+  sps <- Spectra()
+  res <- entropy(sps)
+  expect_identical(res, numeric())
+
+  df <- DataFrame(msLevel = c(1L, 2L), centroided = TRUE)
+  df$intensity <- list(c(5, 9, 3), c(9, 8, 2))
+  df$mz <- list(1:3, 1:3)
+  sps <- Spectra(df)
+
+  res <- entropy(sps)
+  expect_identical(res, c(17, 19))
+
+  sps <- replaceIntensitiesBelow(sps, threshold = 4)
+  res <- entropy(sps)
+  expect_identical(res, c(14, 17))
+})