# peakPantheR v1.2.0

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## Peak Picking and Annotation of High Resolution Experiments

An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files.

# peakPantheR

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

## Overview

peakPantheR implements functions to detect, integrate and report pre-defined features in MS files. 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

## Installation

Install the development version of the package directly from GitHub with:

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


If the dependencies mzR and MSnbase are not successfully installed, Bioconductor must be added to the default repositories with:

setRepositories(ind=1:2)


## Usage

Both real time and parallel compound integration require a common set of information:

• Path(s) to netCDF / mzML MS file(s)
• An expected region of interest (RT / m/z window) for each compound.

## Vignettes

peakPantheR is licensed under the GPLv3

As a summary, the GPLv3 license requires attribution, inclusion of copyright and license information, disclosure of source code and changes. Derivative work must be available under the same terms.