Changelog

Source: NEWS.md

Version 1.3

Changes in 1.3.3

• Major ChromBackendSpectra performance improvements: chromExtract(), Chromatograms(spectra), peaksData() and [ no longer re-validate the wrapped Spectra on every call (which re-stated every backing file), so they no longer scale with the number of files.

• Improve performance of peaksData() for ChromBackendSpectra with overlapping chromatogram windows (e.g. from chromExtract()): each spectrum is aggregated once and shared across the windows it falls in, instead of once per window. Results are unchanged; the speed-up grows with the number of overlapping windows.

• Improve performance of peakBoundary(): valleys flanking the apex are located by scanning outwards from it rather than scanning the whole chromatogram. Results are unchanged.

• Order dataOrigin by first appearance when computing the spectra sort index, consistent with backendParallelFactor().

Changes in 1.3.2

• Change plotChromatograms() and plotChromatogramsOverlay() to methods.
• Import compareChromatograms() from ProtGenerics.

Changes in 1.3.1

• Addition of logo and align to BioC 3.23 release.

• Fix ChromBackendSpectra spectraSortIndex test to shuffle spectra first, avoiding a spurious failure when input data is already sorted.

Version 1.1

Changes in 1.1.8

• Improve performance of matchRtime().

• Fix compareChromatograms(): ... arguments (e.g. tolerance) are now routed to MAPFUN or FUN based on their formal parameters, preventing errors when FUN = cor received unknown arguments.

Changes in 1.1.7

• Improve performance of .prepare_spectra_input(): spectra are now pre-filtered to the non-overlapping union of EIC retention time ranges using MsCoreUtils::reduce() and Spectra::filterRanges(), and peak data is loaded in a single peaksData() call instead of separate mz() and intensity() calls. This reduces I/O and memory usage, especially for file-backed backends.

Changes in 1.1.6

• Add compareChromatograms() and matchRtime() for pairwise similarity of chromatographic intensity profiles.

Changes in 1.1.5

• Add peakBoundary() method for Chromatograms objects. Determines the retention time boundaries of the tallest peak in each chromatogram using MsCoreUtils::valleys() to locate flanking valleys, with a threshold-based fallback. Returns a matrix with left_boundary and right_boundary columns.

Changes in 1.1.4

• setBackend() now clears the processing queue after switching backend, preventing queued processing steps from being applied twice (once during the data transfer and again on subsequent peaksData() calls).

• Fix setBackend() parallel branch (used for ChromBackendMzR) to correctly apply queued processing steps to each chunk before transferring data to the new backend.

• Major performance improvement in .process_peaks_data() for ChromBackendSpectra. Key optimizations include: pre-extracting mz() and intensity() as plain R lists (avoiding slow SimpleNumericList indexing), global retention time pre-filtering, a fast path for TIC/BPC cases, and using findInterval() with cumsum() for m/z range lookups. Combined, setBackend() showed 9x speed up for 1000 chromatograms.

• Add optimized intensity() and rtime() accessors for ChromBackendMemory using direct [[ extraction instead of the slower [, col, drop] path through peaksData().

• Further accessor optimizations: intensity(), rtime(), and lengths() on Chromatograms now bypass peaksData() dispatch when the processing queue is empty. peaksData() on ChromBackendMemory uses a fast [[ path for single-column requests. Direct lengths() methods added for all backends using nrow() instead of going through intensity().

• Replace do.call(rbind, ...) with data.table::rbindlist() in chromExtract() for ChromBackendMemory, ChromBackendMzR, and ChromBackendSpectra for faster row-binding of many data.frames.

• Replace replicate(n, .EMPTY_PEAKS_DATA, simplify = FALSE) with rep(list(.EMPTY_PEAKS_DATA), n) across backends to avoid repeated expression evaluation overhead.

Changes in 1.1.3

• Add filterEmptyChromatograms() function to remove empty chromatograms (i.e., chromatograms without peaks) from a Chromatograms or ChromBackend object.

• Add concatenateChromatograms() function and c() method to combine multiple Chromatograms objects into a single object. Also add split() method to split a Chromatograms object based on a grouping factor.

• Add extrapolate parameter to imputePeaksData() (default FALSE). When TRUE, leading/trailing NA values outside the range of observed data are extrapolated. When FALSE (default), only interpolation is performed and edge NA values remain as NA.

Changes in 1.1.2

• Fix peaksData() for ChromBackendSpectra to return data in the correct row order when multiple chromatograms share the same chromSpectraIndex. This bug caused setBackend() to produce mismatched chromData and peaksData when converting from ChromBackendSpectra to ChromBackendMemory with objects containing multiple EICs.

Changes in 1.1.1

• Aligned the package with the Bioconductor 3.22 release.
• Expanded the vignette to cover ChromBackendSpectra usage, chromatogram extraction with chromExtract(), and imputation workflows via imputePeaksData().
• Added spectraSortIndex() for ChromBackendSpectra to compute the desired retention-time order on demand, avoiding the need to keep on-disk Spectra objects sorted in memory.

Version 0.99

Changes in 0.99.7

• Add chromExtract() method to generate a new Chromatograms object from an existing one by extracting a subset of chromatograms based on retention times (optionally m/z) boundaries.
• Add imputePeaksData() method to impute missing values in the chromatographic peaks data.
• Fix factorize() so that the parameter factorize.by can take a character vector of length 1.

Changes in 0.99.6

• Add Spectra dependency.

Changes in 0.99.5

• Add IRanges dependency

Changes in 0.99.4

• Add dependencies to Vignette.

Changes in 0.99.0

• General documentation and formatting fixes for Bioconductor submission.

Changes in 0.6.0

• Addition of ChromBackendSpectra class and its respective methods.
• Addition of plotChromatograms() and plotChromatogramsOverlay() functions.
• Addition of the extractByIndex implementation in the backends.

Changes in 0.5.0

• Addition of ChromBackendMzR and its respective methods.
• Addition of the Chromatograms vignette, which provides an overview of the object and related functionalities.

Changes in 0.4.0

• Addition of peaksData() and implementation of chunkwise (and therefore paralleled) processing of Chromatograms object.
• Addition of addProcessing(), applyProcessing(), processingChunkFactor(), and processingChunkSize().

Changes in 0.3.0

• Addition of filterChromData() method for ChromBackend.
• Creation of the Chromatograms class and implementation of basic accessor methods.
• Addition of basic plotting functions.

Changes in 0.2.0

• Addition of ChomBackendMemory class and associated methods

Changes in 0.1.0

• Addition of basic ChromBackend class and default methods