% \VignetteIndexEntry{mrbin}
% \VignetteDepends{mrbin}
% \VignetteKeyword{NMR}
% \VignetteKeyword{metabolomics}
\documentclass{article}

\renewcommand*\familydefault{\sfdefault}
\usepackage{graphics}
\usepackage{amsmath}
\usepackage[utf8]{inputenc}
\addtolength{\topmargin}{-2.1cm}
\addtolength{\textheight}{3.8cm}%1.4{.793cm}
\addtolength{\oddsidemargin}{-.875in}
\addtolength{\evensidemargin}{-.875in}
\addtolength{\textwidth}{1.75in}

\begin{document}

\title{mrbin - Magnetic Resonance Binning, Integration and Normalization}
\author{Matthias S. Klein}
\date{Version 1.4.1}
\maketitle
%\tableofcontents
%\pagebreak

\section{Introduction}

Nuclear Magnetic Resonance (NMR) is widely used for metabolomics research. This
package uses spectral binning to convert 1D or 2D NMR data into a matrix of values
suitable for further data analysis and performs basic processing steps in a
reproducible way. Negative values, a common issue in NMR data, are replaced by
positive values. All used parameters are stored in a readable text file and can
be restored from that file to enable exact reproduction of the data at a later
time.\\

\section{Getting Started}

The main functions of this package are controlled via the mrbin() function. Most
other functions in the package will not usually be ever called by the user, but
serve internal purposes. Results returned include the final bin list and a set
of used parameters.\\

\subsection{Installation}

To install  mrbin, please install the latest version of R first. Then install
mrbin.\\

To install the latest stable version of mrbin from CRAN:\\

\begin{verbatim}
install.packages("mrbin")
\end{verbatim}

To install the latest development version from Github:\\

\begin{verbatim}
library(devtools)
install_github("kleinomicslab/mrbin")
\end{verbatim}

To be able to run devtools, you may need to install additional software.\\

After installation, load the package as follows:\\

<<>>=
library(mrbin)
@


\subsection{Prerequisites and Considerations}

To use this package, you will need your NMR data in the Bruker file format
accessible on your computer. Please make sure your data is Fourier transformed,
phase corrected, baseline corrected, and correctly referenced. The data has to
be stored in folders according to standard Bruker folders, that means
foldername/1/pdata/1 etc. Experiment numbers and processing numbers can be
freely chosen.\\

This package has been tested for 1D NOESY and 2D 1H-13C HSQC spectra.\\

Before starting mrbin, take a look at your NMR data, for example in Bruker
Topspin, and decide on the following parameters (you will be able to see the values of
these parameters in regards to your data during running mrbin):\\
\begin{itemize}
  \item Bin area: Area where signals are observed in your data set
  \item Bin width: Should match roughly the width of a singlet peak in your data set. Given in ppm.
  \item Bin height (only 2D): Should match roughly the height of a singlet peak in your data set. Given in ppm.
  \item Solvent area: Area to exclude to remove solvent artifacts
  \item Additional areas to be removed: Any other area containing artifacts, such as streaks surrounding strong peaks.
\end{itemize}

mrbin will also show you preview plots for these parameters during the run.\\


\subsection{Running mrbin in Interactive Mode}

You can start mrbin using the following code:\\

\begin{verbatim}
mrbinResults<-mrbin()
\end{verbatim}

This will start a series of questions that will guide you through the parameters to be used.\\

mrbin() returns an (invisible) list containing three variables:\\

\begin{itemize}
  \item bins: A matrix containing bin data for all samples, Depending on the option you chose, the data will be cleaned up and scaled.
  \item parameters: A list containing all parameters used to create the bin matrix.
  \item factors: A vector containing group names for all samples.
\end{itemize}

Up to three files may be written to the chosen directory:\\
\begin{itemize}
  \item A .txt file containing all parameters. This file can be reloaded to R using recreatemrbin("filename"). This will enable reusing parameters used in a previous run and can help increase reproducibility.
  \item A .csv file containing the bin data for use in other software tools.
  \item A .pdf file containing quality control plots, including a PCA plot
\end{itemize}

\subsection{Recreating Data and Parameters}
In order to create reproducible results, mrbin will save the used parameters to
a text file. Please keep this file. You may want to share this file in a data
repository when publishing your findings.\\

While it is fine to view the parameter text file in a text editor, please do not
change its contents, as this may break its formatting.\\

In order to recreate a previous data set, or to reload previously used
parameters, use:

\begin{verbatim}
mrbinResults<-mrbin()
\end{verbatim}

and select ""Reload from file" when asked "Set parameters or use existing
parameters?". This will restore all parameters that were previously used. If the
file was created using an older version of mrbin, this may cause inconsistencies.
Missing parameters will be added using standard parameters. Ideally, download the
older mrbin version at kleinomicslab.com and use the old version to recreated the
data in an exact way.\\

Please be aware that bins will have to be recalculated, so the original NMR
spectra will have to be present to do this.\\

\subsection{Setting Parameters at the Command Line}
Parameters can be submitted at the command line. When using silent=TRUE, this will
set up all parameters and run all steps without asking for user input.\\

When setting silent=FALSE, the user will be guided through the user input
questionnaire to make adjustments to the submitted parameters.\\

\subsubsection{Example: 1D Data}

The following example provides all parameters for analyzing a 1D data set.\\

<<>>=
mrbinResults<-mrbin(silent=TRUE,
     setDefault=FALSE,
     parameters=list(verbose=TRUE,
             dimension="1D",
             binMethod="Rectangular bins",
             binwidth1D=.01,
             referenceScaling="Yes",
             removeSolvent="Yes",
             removeAreas="No",
             sumBins="No",
             noiseRemoval="Yes",
             PQNScaling="Yes",
             fixNegatives="Yes",
             logTrafo="Yes",
             saveFiles="Yes",
             NMRfolders=c(system.file("extdata/1/10/pdata/10",package="mrbin"),
                          system.file("extdata/2/10/pdata/10",package="mrbin"),
                          system.file("extdata/3/10/pdata/10",package="mrbin"))
     ))
@

This example uses data from the mrbin package. To use your own data, add
the full folder names of the Bruker folders holding the files "1r" (or "2rr" for
2D data) as follows:

\begin{verbatim}
NMRfolders=c("C:/Bruker/TopSpin3.6.1/data/guest/nmr/sample_1/10/pdata/10",
             "C:/Bruker/TopSpin3.6.1/data/guest/nmr/sample_2/10/pdata/10",
             "C:/Bruker/TopSpin3.6.1/data/guest/nmr/sample_3/10/pdata/10")
\end{verbatim}

\subsubsection{Example: 2D Data}

The following example provides all parameters for analyzing a 2D data set.\\

<<>>=
mrbinResults<-mrbin(silent=TRUE,
     setDefault=FALSE,
     parameters=list(verbose=TRUE,
               dimension="2D",
               binwidth2D=0.1,
               binheight=3,
               PQNScaling="No",
               fixNegatives="No",
               logTrafo="No",
               signal_to_noise2D=20,
               NMRfolders=c(system.file("extdata/1/12/pdata/10",package="mrbin"),
                       system.file("extdata/2/12/pdata/10",package="mrbin"),
                       system.file("extdata/3/12/pdata/10",package="mrbin"))
               ))
@

This example uses data from the mrbin package. To use your own data, add
the full folder names of the Bruker folders holding the files "1r" (or "2rr" for
2D data) as follows:

\begin{verbatim}
NMRfolders=c("C:/Bruker/TopSpin3.6.1/data/guest/nmr/sample_1/12/pdata/10",
             "C:/Bruker/TopSpin3.6.1/data/guest/nmr/sample_2/12/pdata/10",
             "C:/Bruker/TopSpin3.6.1/data/guest/nmr/sample_3/12/pdata/10")
\end{verbatim}

The binned NMR data can be found in mrbinResults\$bins. This numeric matrix contains
bins in columns and samples in rows, and can be directly used for further data
analysis.\\

The binned data can also be loaded from the hard drive later (if an output file
was specified):

\begin{verbatim}
binData<-read.csv("C:/Users/User/Documents/mrbin_bins.csv",
                  check.names = FALSE, row.names=1)
\end{verbatim}

Column names include left and right borders or each bin separated by commas. For
2D data, column names include left, right, top, and bottom border of each bin.\\
\pagebreak

\subsubsection{Example: Lipid Data Analysis}

Analyzing lipid NMR signals can be accomplished using custom bin lists rather
than a regular grid of bins. This can be done as in the following code:\\

<<>>=
results <- mrbin(silent=TRUE,parameters=list(binMethod="Custom bin list",
 dimension="1D",specialBinList=matrix(c(
                               5.45,5.2,0,160,
                               2.9,2.74,0,160,
                               2.14,1.93,0,160,
                               1.41,1.2,0,160,
                               0.94,0.8,0,160,
                               2.44,2.2,0,160,
                               4.325,4.26,0,160
                               ),ncol=4,byrow=TRUE,dimnames=list(c(
                               "-CH=CH- Methene",
                               "=CH-CH2-CH= Diallylic",
                               "-CH2-CH=CH- Allylic",
                               "-CH2- Methylene",
                               "-CH3 Methyl",
                               "COO-CH2-CH2- Methylene_to_carboxyl",
                               "Glycerol"
                               ),NULL)),
 referenceScaling="Yes",reference1D=c(0.03,-0.03),removeSolvent="No",
 removeAreas="No",sumBins="No",trimZeros="Yes",noiseRemoval="No",
 PQNScaling="No",fixNegatives="Yes",logTrafo="No",defineGroups="No",PCA="Yes",
 createBins="Yes",useAsNames="Folder names",saveFiles="No",verbose=TRUE,
 NMRfolders=c(system.file("extdata/1/10/pdata/10",package="mrbin"),
              system.file("extdata/2/10/pdata/10",package="mrbin"),
              system.file("extdata/3/10/pdata/10",package="mrbin"))
 ))
@

When using custom bin lists, each spectral data point may be part of multiple
bins. For rectangular bin lists, each data point can only be counted once. The
lipid signal areas used in this example are based on Klein et al, 2011.\\

\subsection{mrbin Workflow}

The sequence of data processing is as follows:\\

\begin{itemize}
  \item Gathering all parameters from user
  \item Creating a set with coordinates of each bin
  \item Removing solvent region
  \item Removing additional regions
  \item Cropping of HSQC spectra to the region along the diagonal
  \item Summing or merging regions containing peaks with unstable positions such as citric acid
  \item Reading Bruker NMR data
  \item Scaling to reference region
  \item Binning
  \item Removal of bins containing mostly noise
  \item PQN transformation
  \item Replacement of negative values
  \item Log transform
  \item Plotting a quality control plot, including a PCA plot
  \item Saving bins, parameters and the plot to the hard drive
\end{itemize}

\subsection{Affine Transformation of Negative Values}

The function atnv replaces (column-wise) negative values by a small positive
number. The number is calculated as an affine transformation to the range of
the lowest positive number to 0,01*the lowest positive number (of this
column). Ranks stay unchanged. Positive numbers are not altered.\\

If sample-wise noise levels are available, the median noise level of samples
with negative values is calculated and replaces the lowest positive number in
case it is smaller. If no noise data is available, the 1\% percentile of all
positive values in the data set is used as an estimate.\\

It is recommended to use this function AFTER noise removal and other data
clean-up methods, as it may alter (reduce) the noise level of the binned data.
If no NMR data and noise levels are provided as arguments, the function will
use NMR data and noise levels from the global variables mrbin.env\$bins and
mrbin.env\$mrbinTMP.\\

To use own (user provided) data:\\

\begin{verbatim}
atnv(NMRdataMatrix,noiseLevelVector)
\end{verbatim}

To use current mrbin data from the internal memory, use atnv()) without
parameters. This requires data loaded
using mrbin(). This is usually not necessary as it is included in the mrbin work
flow.\\


\subsection{Plotting}

The mrbin package contains basic plotting commands for 1D and 2D NMR data.\\

To use these, you need to first load one NMR spectrum:

\begin{verbatim}
readBruker(dimension="1D",folder=system.file("extdata/1/10/pdata/10",package="mrbin"))
plotNMR()
\end{verbatim}

The system.file command loads example data from the mrbin package. To use your own
spectra, please adjust as follows:\\

\begin{verbatim}
readBruker(dimension="1D",folder="C:/Bruker/TopSpin3.6.1/data/guest/nmr/sample_1/12/pdata/10")
plotNMR()
\end{verbatim}


For 2D data, this code reads as follows:

\begin{verbatim}
readBruker(dimension="2D",folder=system.file("extdata/1/12/pdata/10",package="mrbin"))
plotNMR()
\end{verbatim}


There are multiple command for editing the plot:

\begin{verbatim}
zoom(left=4.6, right=2, top=10, bottom=150) #Exact zoom
zoomIn() #Zoom in
zoomOut() #Zoom out
intPlus() #Increase intensity
intMin() #Decrease intensity
left() #Move spectrum to the left
right() #Move spectrum to the right
\end{verbatim}

For 2D data, you can additionally use the following commands:

\begin{verbatim}
contMin() #Decrease minimum contour level (show more small peaks)
contPlus() #Increase minimum contour level (remove small peaks)
up() #Move spectrum up
down() #Move spectrum down
\end{verbatim}


\section{Known Issues}

\subsection{Pop-Up Windows}
mrbin is set up to ask for user input through pop-up windows. This requires
graphics support, otherwise the user input will be asked through command line
menus, which is less user friendly but still offers the full functionality.\\

\subsection{Apple/Mac Computers And RStudio}
In some cases, running mrbin from within RStudio on Apple computers will not
generate pop-up windows. To enable pop-up windows, it might be helpful to install
the newest version of xquartz from https://www.xquartz.org.\\

\section{License}

This project is licensed under GPL-3.0.\\

\section{References}

\textbf{Klein MS}, Dorn C, Saugspier M, Hellerbrand C, Oefner PJ \& Gronwald W
(2011): Discrimination of Steatosis and NASH in Mice Using Nuclear Magnetic
Resonance Spectroscopy. \textit{Metabolomics} 7:237-246\\

\end{document}

