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

More information is available in the following vignettes:

Copyright

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.