mrbin News

Version 1.6.4

Minor changes in calculations in the fia function. Features of lowest impact now are assigned a (large) FIA score instead of an NA value

Bin intensities are now pseudo-integrals (mean of data points times range (1D), or times area (2D)). So far, intensities were the mean of data points in the bin range. For simple rectangular bins, results are identical apart from a scaling factor, so most data analysis methods will give identical results. To enforce the old behavior, use mrbin(parameters=list(useMeanIntensityForBins=TRUE))
Multiple spectra are now shown in previews to visualize sample-to-sample variability
PCA plots: When using more groups than available symbols (from pch), letter are now used to mark the groups. This also removes the warning messages generated in these cases.
Reading spectra without title does no longer create an error in readBruker(), however, such spectra are still not shown in the spectrum browser as they are usually not of interest
Before binning, folder list is checked to find missing folders. This is to avoid long calculation that end with a “could not open file” error. This uses the new readBruker() parameter checkFiles.
Speed improvements for displaying and saving the final results plot
New plotting function mrplot()
RStudio plotting issue solved: Plots are now refreshed so the current plot is displayed timely

Speed improvements for 1D spectra
New quality check function checkBaseline: For severe baseline distortions in noise region, a warning is displayed
New quality check in function binMultiNMR2: For severe baseline distortions in the reference region, the reference peak integral might be negative. In this case,a warning is displayed and the absolute value is used instead
New quality check function binMultiNMR2: If reference scaling is used and the reference signal intensity is unexpectedly low, a warning is displayed
If quality check warnings are generated during a run, the warnings are saved in the parameter text file for later viewing

Small improvement in spectrum browsing. Experiments with no title file are no longer displayed during browsing, as these are usually uninformative pulse calibration data
Added a message recommending installing xquartz on Apple computers
Citation information was added

An error in reference scaling was fixed, this prevented reference scaling in some cases
PQN scaling is now performed after fixing negative values by atnv() (previously: before atnv). This might slightly change PQN scaling results in rare cases
Speed improvements by adding optional support for parallel computing using the parallel package

Noise levels per bin are no longer saved in the .txt file to keep this file clear and tidy. Instead, raw noise levels and median noise levels (adjusted for bin size) are now saved in the output .txt file

Summed bins are now calculated with the exact defined borders. Surrounding bins are truncated
Noise levels are now calculated separately for each bin in each spectrum, correcting for differences in data points per bin
PCA plot labels now show percentage of variance instead of percentage of standard deviation
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability, especially when analyzing single samples and/or single bins

Vignette was expanded
Bin borders are now rounded to avoid floating point inconsistencies
PQN normalization now also ignores glucose signals in 1D spectra. This behavior can be turned off now as well.
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability, especially when analyzing single samples and/or single bins

Solvent region change: Only bins that are completely within the solvent region are removed
Excluded regions: No NMR data from excluded regions or solvent regions is now used to calculate bins, even if the bin overlaps with the excluded region
New trimming function to remove bins that have mostly values of zero; These are created at the edges of the spectrum and at edges of removed regions
A vignette was added
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability

Noise is now estimated from raw data points (not bin values) and mean number of data points per bin
New noise calculations tend to be lower than the previous estimates. SNR levels may need to be increased by a factor of 2.5. Default SNR levels have been raised to reflect this.
Solvent region change: Any bins that contain any part of these regions are removed (previously only if mean of bin was within region)
Added new way of creating sample names from EXPNO and folder name
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability
Speed improvements

Default 1D noise range was changed to 10 - 9.5 ppm (was 10-9.4). Default 1D binning area changed to 10-0.5 (was 9.5-0.5)
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability

All parameters can now be conveniently set from the command line by passing a list of parameters to mrbin()
Special bin regions can now be defined instead of rectangular bins, e.g. for lipid analysis
mrbin() now returns the group factors as an additional element “factors” in the returned list
New function setCurrentSpectrum() to set current spectrum, e.g. for plotting
Reloading a parameter set from a file now checks whether all required parameters have been set and adds missing ones
Results plots are nicer now. A new plot shows which regions were left after all processing steps.
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability