@@ -1,6 +1,6 @@

 Package: MsCoreUtils

 Title: Core Utils for Mass Spectrometry Data

-Version: 1.11.6

+Version: 1.11.7

 Description: MsCoreUtils defines low-level functions for mass

     spectrometry data and is independent of any high-level data

     structures. These functions include mass spectra processing

@@ -38,6 +38,10 @@ Authors@R: c(person(given = "RforMassSpectrometry Package Maintainer",

              person(given = "Roger", family = "Gine Bertomeu",

                     email = "roger.gine@iispv.cat",

                     comment = c(ORCID = "0000-0003-0288-9619"),

+                    role = "ctb")),

+             person(given = "Mar", family = "Garcia-Aloy",

+                    email = "mar.garcia@fmach.it",

+                    comment = c(ORCID = "0000-0002-1330-6610"),

                     role = "ctb"))

 Depends:

     R (>= 3.6.0)

@@ -1,5 +1,9 @@

 # MsCoreUtils 1.11

+## MsCoreUtils 1.11.7

+

+- Add functions `entropy` and `nentropy`.

+  

 ## MsCoreUtils 1.11.6

 - Fix bug in `impute_MinDet(MARGIN = 1)` and add unit test.

@@ -2,11 +2,19 @@

 #'

 #' @description

 #'

-#' These functions allows to calculate entropy measurements of an MS/MS  

+#' These functions allow to calculate entropy measurements of an MS/MS  

 #' spectrum based on the metrics suggested by 

 #' Li et al. (https://doi.org/10.1038/s41592-021-01331-z).

+#' Spectral entropy and normalized entropy are used to measure the complexity 

+#' of an spectra.

+#' MassBank of North America (MoNA) defines spectra entropy as the intensity 

+#' weighted spectral peak number 

+#' (https://mona.fiehnlab.ucdavis.edu/documentation/entropy. 

+#' Additionally it is suggested to label as low-quality spectrums the ones 

+#' that have a normalized entropy higher than 0.8 and spectral entropy 

+#' higher than 3. 

 #'

-#' @param x `numeric`, intensities of the fragment ions value(s).

+#' @param x `numeric`, intensities of the fragment ions(s).

 #'

 #' @return `numeric`: (normalized) entropy `x`.

 #'

@@ -26,15 +34,14 @@

 #' @examples

 #' spectrum <- rbind(c(41.04, 37.16), c(69.07, 66.83), c(86.1, 999.0))

 #'

-#' entropy_spectral(spectrum[,2])

-#' entropy_normalized(spectrum[,2])

+#' entropy(spectrum[,2])

+#' nentropy(spectrum[,2])

 #' 

-entropy_spectral <- function(x){

+entropy <- function(x) {

   y <- x / sum(x)

-  z <- y*log(y)

-  return(-sum(z))

+  -sum(y * log(y))

 }

-entropy_normalized <- function(x){

-  entropy_spectral(x) / log(length(x))

+nentropy <- function(x) {

+  entropy(x) / log(length(x))

 }

\ No newline at end of file