NEWS.md

In zeehio/MassSpecWavelet: Peak Detection for Mass Spectrometry data using wavelet-based algorithms

MassSpecWavelet 1.65.1 (2023-04-07)

• Fix .Call() for R-4.3. Thanks to Steffen Neumann. Closes #5

MassSpecWavelet 1.64.1 (2023-01-30)

• Fix undefined variable in MassSpecWavelet.Rmd

MassSpecWavelet 1.63.6 (2022-10-15)

• Fix regression in cwt() when scales has length 1.

MassSpecWavelet 1.63.5 (2022-10-11)

• getRidge() supports a scaleToWinSize parameter. This argument controls how scales get mapped to window sizes. These windows are used to track the local maxima into ridges. MassSpecWavelet had a criteria of winsize <- 2*scale+1, while xcms modified it to winsize <- floor(scale/2). This new argument enables xcms maintainers to call MassSpecWavelet's getRidge (if they want to) using their criteria, while it still lets us preserve backwards compatibility in our results. See ?getRidge for further details.

• The getLocalMaximumCWT() is_amp_thres_relative parameter is now isAmpThreshRelative, for consistency with other parameter capitalization in the package. Since it was introduced 10 days ago, I don't think there will be more than one user using it.

• getLocalMaximumCWT() and peakDetectionCWT have a exclude0scaleAmpThresh parameter. When computing the relative amp.Th, if this parameter is set to TRUE, the amp.Th will exclude the zero-th scale from the max(wCoefs). The zero-th scale corresponds to the original signal, that may have a much larger baseline than the wavelet coefficients and can distort the threshold calculation. The default value is FALSE to preserve backwards compatibility.

• peakDetectionCWT lets the user pass custom arguments to getRidge().

MassSpecWavelet 1.63.4 (2022-10-10)

• The improvements in localMaxima() and cwt() provide significant speed-ups to peakDetectionCWT() as well as better scalability.

• A prepareWavelets() function lets the user pre-compute the daughter wavelets for more efficient cwt() calculations when applied on multiple spectra. When used transforming 1000 spectra, of 2000 points long each, using 25 different scales, cwt() is twice as fast as in previous versions. Further improvements to avoid some memory allocations are still feasible in future versions.

• Through the prepareWavelets() function, we provide the extendLengthScales argument, that provides the same functionality than the extendLengthMSW argument in xcms:::MSW.cwt().

• The peakDetectionCWT() function accepts a prepared_wavelets object in the scales argument for better efficiency.

MassSpecWavelet 1.63.3 (2022-10-10)

• localMaxima() has a more efficient implementation of the algorithm, now being 10x faster than before, while giving the same results.

• Experimentally, localMaxima() can use a new and different algorithm for detecting local maxima. See the new "Finding local maxima" vignette for further details.

MassSpecWavelet 1.63.2 (2022-09-29)

• Let getLocalMaximumCWT() have a relative amp.Th. Related to #4.
• Fix bug on identifyMajorPeaks() where nearbyWinSize was forced to 150 if nearbyPeak was set to TRUE. Related to #4.
• Added excludeBoundariesSize argument to identifyMajorPeaks(). Before, nearbyWinSize was used for two different but related criteria: the range for including peaks close to a large peak AND the range to exclude peaks close to the beginning and end of the signal. Now, we have two independent arguments for each setting. The current behaviour does not change, but it is now more flexible. Related to #4.

MassSpecWavelet 1.63.1 (2022-07-08)

• Drop sav.gol alias from the documentation. Related to #2
• Explain how the scales argument is defined in relation to the mother wavelet.
• Add sessionInfo() to the vignette

MassSpecWavelet 1.61.3 (2022-04-05)

• Add signal to Suggests. Replace sav.gol() with signal::sgolayfilt(). Closes #2
• Minor documentation improvements

MassSpecWavelet 1.61.2 (2022-04-04)

• Remove xcms and caTools. Those are great packages but we don't use them directly in MassSpecWavelet.
• Replace Sweave with RMarkdown vignette and update styles with BiocStyle

MassSpecWavelet 1.61.1 (2022-04-01)

• Change Maintainer to Sergio Oller
• Add NEWS.md file
• Fix warning (error on R>=4.2) when cwt() has a matrix in the wavelet argument
• Fix warning due to partial matching of arguments inside cwt()
• Move waveslim from Depends to Suggests
• Make all calls to recommended packages qualified (e.g. sd -> stats::sd)
• Remove empty sections in man/ files.
• Register C routines

zeehio/MassSpecWavelet documentation built on May 6, 2023, 1:32 a.m.