Package: peakPantheR
Authors: Arnaud Wolfer

Package for Peak Picking and ANnoTation of High resolution Experiments in R, implemented in R and Shiny

1 Overview

peakPantheR implements functions to detect, integrate and report pre-defined features in MS files (e.g. compounds, fragments, adducts, …).

It is designed for:

  • Real time feature detection and integration (see Real Time Annotation)
    • process multiple compounds in one file at a time
  • Post-acquisition feature detection, integration and reporting (see Parallel Annotation)
    • process multiple compounds in multiple files in parallel, store results in a single object

peakPantheR can process LC/MS data files in NetCDF, mzML/mzXML and mzData format as data import is achieved using Bioconductor’s mzR package.

2 Installation

To install peakPantheR from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("peakPantheR")

Install the development version of peakPantheR directly from GitHub with:

# Install devtools
if(!require("devtools")) install.packages("devtools")
devtools::install_github("phenomecentre/peakPantheR")

2.1 Getting Started

To get started peakPantheR’s graphical user interface implements all the functions to detect and integrate multiple compounds in multiple files in parallel and store results in a single object. It can be employed to integrate a large number of expected features across a dataset:

library(peakPantheR)

peakPantheR_start_GUI(browser = TRUE)
#  To exit press ESC in the command line