Detection of Isotope Pattern of a Mass Spectrometric Measurement

Provides a low-level interface for a deisotoper container implemented in the 'Java' programming language and means of S3 helper functions for plotting and debugging isotopes of mass spectrometric data. The deisotoper algorithm detects and aggregates peaks which belong to the same isotopic cluster of a given mass spectrum.

deisotoper

This package contains a Java implementation of

• Features Based Deisotoping Method

Installation

from github

Install the latest development version:

install.packages(c('rJava', 'devtools', 'DiagrammeR', 'lattice', 'roxygen2',
          'protViz', 'shiny', 'testthat', 'knitr'))
library(devtools)
install_git('https://github.com/protViz/deisotoper', build_vignettes = TRUE, quiet = FALSE)

sudo R CMD javareconf

from deisotoper_0.0.3.tar.gz

Install the latest JDK(>= 8.0) and R(>=3.3). Then run in R:

install.packages(c('rJava', 'devtools', 'DiagrammeR', 'lattice', 'roxygen2',
          'protViz', 'shiny', 'testthat', 'knitr'))
install.packages("~/deisotoper_0.0.3.tar.gz", repos = NULL, type = "source")

sudo R CMD javareconf

from CRAN

Install the latest JDK(>= 8.0) and R(>=3.3). Then run in R:

install.packages(c('rJava', 'devtools', 'DiagrammeR', 'lattice', 'roxygen2',
          'protViz', 'shiny', 'testthat', 'knitr'))
install.packages("deisotoper")

sudo R CMD javareconf

Documentation

The package ships with a package vignette browseVignettes('deisotoper') (>=0.0.2) and a reference manual (just type ?deisotoper on the R shell).