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

 Package: MsCoreUtils

 Title: Core Utils for Mass Spectrometry Data

-Version: 1.15.2

+Version: 1.15.3

 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

@@ -76,4 +76,4 @@ BugReports: https://github.com/RforMassSpectrometry/MsCoreUtils/issues

 URL: https://github.com/RforMassSpectrometry/MsCoreUtils

 biocViews: Infrastructure, Proteomics, MassSpectrometry, Metabolomics

 Roxygen: list(markdown=TRUE)

-RoxygenNote: 7.2.3

+RoxygenNote: 7.3.1

@@ -6,6 +6,7 @@ export(aggregate_by_vector)

 export(asInteger)

 export(between)

 export(bin)

+export(breaks_ppm)

 export(closest)

 export(coefMA)

 export(coefSG)

@@ -1,8 +1,13 @@

 # MsCoreUtils 1.15

+## MsCoreUtils 1.15.3

+

+- Add function `breaks_ppm` to create a sequence of numbers with increasing

+  difference between elements (defined by parameter `ppm`).

+

 ## MsCoreUtils 1.15.2

-- Porting baseline baseline estimation function (see [issue

+- Porting baseline estimation function (see [issue

   119](https://github.com/rformassspectrometry/MsCoreUtils/issues/119)).

 ## MsCoreUtils 1.15.1

@@ -135,6 +135,8 @@ bin <- function(x, y, size = 1,

 #' @return `numeric` with the sequence of values with increasing differences.

 #'     The returned values include `from` and `to`.

 #'

+#' @export

+#'

 #' @author Johannes Rainer

 #'

 #' @examples

@@ -23,7 +23,8 @@ thrown.}

 \item{size}{\code{numeric(1)} with the size of a bin.}

-\item{breaks}{\code{numeric} defining the breaks (bins).}

+\item{breaks}{\code{numeric} defining the breaks (bins). See \code{\link[=breaks_ppm]{breaks_ppm()}} to

+define breaks with increasing size (depending on ppm).}

 \item{FUN}{\code{function} to be used to aggregate values of \code{x} falling into the

 bins defined by \code{breaks}. \code{FUN} is expected to return a \code{numeric(1)}.}

new file mode 100644

@@ -0,0 +1,53 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/binning.R

+\name{breaks_ppm}

+\alias{breaks_ppm}

+\title{Sequence with increasing difference between elements}

+\usage{

+breaks_ppm(from = 1, to = 1, by = 1, ppm = 0)

+}

+\arguments{

+\item{from}{\code{numeric(1)} with the value from which the sequence should start.}

+

+\item{to}{\code{numeric(1)} defining the upper bound of the sequence. Note that

+the last value of the result will not be equal to \code{to} but equal to the

+first number in the sequence which is larger than this value.}

+

+\item{by}{\code{numeric(1)} defining the constant part of the difference by which

+numbers should increase.}

+

+\item{ppm}{\code{numeric(1)} defining the variable part of the difference by

+which numbers should increase (expressed in parts-per-million of the

+values).}

+}

+\value{

+\code{numeric} with the sequence of values with increasing differences.

+The returned values include \code{from} and \code{to}.

+}

+\description{

+\code{breaks_ppm} creates a sequence of numbers with increasing differences

+between them. Parameter \code{ppm} defines the amount by which the difference

+between values increases. The value for an element \code{i+1} is calculated by

+adding \code{size} to the value of element \code{i} and in addition also the

+\code{ppm(a, ppm)}, where \code{a} is the value of the element \code{i} plus \code{size}. This

+iterative calculation is stopped once the value of an element is larger

+than \code{to}. The last value in the result vector will thus not be equal to

+\code{to} (which is in contrast to the base \code{\link[=seq]{seq()}} function) but slightly

+higher.

+

+A typical use case of this function would be to calculate breaks for the

+binning of m/z values of mass spectra. This function allows to create

+m/z-relative bin sizes which better represents measurement errors observed

+on certain mass spectrometry instruments.

+}

+\examples{

+

+res <- breaks_ppm(20, 50, by = 1, ppm = 50)

+res

+

+## difference between the values increases (by ppm)

+diff(res)

+}

+\author{

+Johannes Rainer

+}