1 Introduction

This document provides a brief summary on how to use the PepsNMR package. In this package, pre-processing functions transform raw FID signals from 1H NMR spectroscopy into a set of interpretable spectra.

2 Installation

The PepsNMR package is available on Bioconductor and can be installed via BiocManager::install:

if (!requireNamespace("BiocManager", quietly = TRUE))

                     dependencies = c("Depends", "Imports", "Suggests"))

Note tha installing the Suggests dependencies will install the PepsNMRData package to run the demo below.

The package needs to be loaded once installed to be used:


The package development version is available on Github (Master branch): https://github.com/ManonMartin/PepsNMR, although it is highly recommended to rely on the Bioconductor release version of the package to avoid any package version mismatch.

3 Data importation

The first step is meant to access the raw data files. To import Free Induction Decays (FIDs) in Bruker format, use the ReadFids function. This function will return a list with the FID data matrix (saved in Fid_data) and metadata about these FIDs (saved in Fid_info).

fidList <- ReadFids(file.path(path,dataset_name)) 

Fid_data <- fidList[["Fid_data"]]
Fid_info <- fidList[["Fid_info"]]

The possible directory structures are illustrated here: