mrbin News
Version 1.6.5
- New output of fia function: scoresIndividual shows fia score for
each tested sample
- Speed improvements in the fia function
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
Version 1.6.3
- Small bug fixes in the fia function
- Small bug fixes in the mrplot function
Version 1.6.2
- New function fia for analyzing predictive metabolomics models
- Small bug fixes in the mrplot function
Version 1.6.1
- Small bug fixes in the mrplot function
Version 1.6.0
- 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
Version 1.5.2
- 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
Version 1.5.1
- 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
Version 1.5.0
- 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
Version 1.4.4
- Function PQNScaling now works with externally provided data
- Minor improvements for user friendliness
Version 1.4.3
- 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
Version 1.4.2
- 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
Version 1.4.1
- 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
Version 1.4.0
- 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
Version 1.3.0
- 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
Version 1.2.0
- 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
Version 1.1.0
- 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