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Binning, Scaling and Normalization of NMR Data
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README.md

mrbin - Magnetic Resonance Binning, Integration and Normalization

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.

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.

Installation

To install mrbin, please install the latest version of R first. Then install the package as follows:

To install the latest stable version from CRAN:

install.packages("mrbin")

To install the latest development version from Github:

library(devtools)
install_github("kleinomicslab/mrbin")

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

Running

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:

  • Bin area: Area where signals are observed in your data set
  • Bin width: Should match roughly the width of a singlet peak in your data set. Given in ppm.
  • Bin height (only 2D): Should match roughly the height of a singlet peak in your data set. Given in ppm.
  • Solvent area: Area to exclude to remove solvent artifacts
  • Additional areas to be removed: Any other area containing artifacts, such as streaks surrounding strong peaks.

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

You can start mrbin using the following code:

library("mrbin")
mrbinResults<-mrbin()

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

The sequence of data processing is as follows:

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

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

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

Up to three files may be written to the chosen directory:

  • 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.
  • A .csv file containing the bin data for use in other software tools.
  • A .pdf file containing quality control plots, including a PCA plot

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:

mrbin()

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.

Submitting Parameters at the Command Line

Parameters can be submitted at the command line, using the following syntax:

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("C:/NMR/Sample01/1/pdata/1",
                          "C:/NMR/Sample19/1/pdata/1",
                          "C:/NMR/Sample61/1/pdata/1")
     ))

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 parameters.

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 data:

atnv(NMRdataMatrix,noiseLevelVector)

To use current mrbin data, use the following syntax. This requires data loaded using mrbin(). This is usually not necessary as it is included in the mrbin work flow.

atnv()

Known Issues

Pop-Up Windows

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

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.

Built With

  • [roxygen2]
  • [devtools]

Authors

License

This project is licensed under GPL-3.0.

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