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NEWS.md

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AlpsNMR 4.7.2 (2024-08-10)

  • Disable nested parallellization in nmr_detect_peaks_tune_snr().

AlpsNMR 4.7.1 (2024-06-02)

  • Added nmr_autophase() for automated phase correction using the NMRphasing package (#68).
  • Added to_ASICS function to export dataset for ASICS quantification (#68).

AlpsNMR 4.1.6 (2023-02-16)

  • Download improvements:
    • Progress bar
    • Detect user interruptions
    • Sleep 3 seconds between retrying failed downloads

AlpsNMR 4.1.5 (2023-02-10)

  • Replace deprecated dplyr::select() calls.
  • Remove workaround for mixOmics bug, bump mixOmics dependency
  • Simplify implementation (same algorithm) for determining the optimal number of latent variables in the plsda models.
  • Bump dplyr dependency version.

AlpsNMR 4.1.4 (2022-11-08)

  • Disable nested parallelization
  • Update workaround Biocparallel bpmapply
  • Revert bpstop to sleep

AlpsNMR 4.1.3 (2022-11-07)

  • Closer to the fix

AlpsNMR 4.1.2 (2022-11-04)

  • Try a more robust fix on palomino4 (bpstop() instead sleep)
  • Use register() in an example to avoid further breakage on palomino
  • Workaround performance issues on BiocParallel::bpmapply() (Bioconductor/BiocParallel#228)

AlpsNMR 4.1.1 (2022-11-02)

  • Remove archive dependency
  • Try fixing build on palomino4, due to race condition in R CMD check

AlpsNMR 3.99.7 (2022-10-27)

Minor changes

  • Fix build issue on palomino4, simplifying helper function

AlpsNMR 3.99.6 (2022-10-26)

Minor changes

  • When saving, normalize extra information is saved as well.
  • Updated downsampled demo data for examples.
  • More robust nmr_baseline_threshold()
  • Faster examples

AlpsNMR 3.99.5 (2022-10-26)

Minor changes

  • Remove call to deprecated ggplot2::qplot()

AlpsNMR 3.99.4 (2022-10-19)

Major changes

  • Improved the download_MTBLS242() function, allowing to either download the parts of MTBLS242 needed for the tutorial or the whole dataset, which may be nice to have if you want to play beyond the tutorial.

  • When reading a Bruker sample from a zip file, you now can specify in the file name the zip subdirectory. For instance, "/path/to/sample.zip!/sample/3", when sample.zip contains a folder named sample with a subfolder named 3 that includes the sample data you want to actually read.

Minor changes

AlpsNMR 3.99.3 (2022-10-17)

  • Add libarchive as a SystemRequirement to workaround a limitation of the Bioconductor build system (BBS), that can't pick system requirements recursively. Thanks to Jennifer Wokaty for checking the BBS and providing this suggestion.

AlpsNMR 3.99.2 (2022-10-14)

Breaking changes

  • Set fix_baseline = FALSE in nmr_integrate_regions() as default. The former TRUE approach here did not make much sense if peak boundaries were not perfectly established.

Major changes

  • Baseline estimation: We now offer nmr_baseline_estimation() besides nmr_baseline_removal(). The estimation function computes the baseline and saves it instead of subtracting it from the signal. This is a better approach because it lets each step of the pipeline decide whether it makes sense to subtract the baseline or not. The nmr_baseline_removal() is for now still available, but it will be deprecated in a future version.

  • For the baselineThresh argument in nmr_detect_peaks() we now suggest using nmr_baseline_threshold(dataset, method = "median3mad"). This is more robust than the former (but still the default) method.

  • Peak detection and integration: We want to approach the peak detection, clustering an integration in a different way. While the old pipeline still works as expected, we have introduced new arguments to peak detection, with backwards compatible defaults and a peak clustering function. We still provide the vignette with the former workflow, because it is still relevant but we may deprecate it in a future version, once we are confident the changes we are making are robust across several datasets.

  • Parallellization: We are switching from the future package to BiocParallel, to better integrate in the Bioconductor ecosystem. In this version, if you use a different future plan you may get a warning to switch to BiocParallel. In a future version we will remove our dependency with the (awesome) future package.

Minor changes

  • You can now set experiment names (NMRExperiment) with names(dataset) <- c("Sample1", "Sample2").
  • You can now pass a named vector with the sample names to the nmr_read_samples function. The names will be used as the sample names.
  • Peak detection has a more robust baseline threshold estimation
  • Peak detection estimates the baseline threshold on each sample individually. The threshold is calculated using only the sample where we are currently detecting the peaks.
  • Peak detection includes a simple but effective lorentzian fitting (for area and width estimation)
  • Add functions to evaluate the quality of the peak detection using plots
  • More fine grained interpolation axis if axis = NULL is given in nmr_interpolate_1D()
  • Save list of excluded regions in the nmr_dataset object.
  • Drop MassSpecWavelet workaround on partial argument matching since it was fixed upstream
  • Documentation: Start providing verbose messages with tips in functions
  • Remove unused deprecated imports from the future package (#65, thanks to @HenrikBengtsson)
  • Add URL and BugReports to the DESCRIPTION (#64, thanks to @HenrikBengtsson)
  • Reading bruker samples is now a bit more robust and gives detailed tracebacks in case of error.

AlpsNMR 3.5.1 (2022-04-07)

  • plot_interactive now accepts an overwrite argument to avoid asking the user interactively
  • Improve nmr_detect_peaks_tune_snr to tune the SNR threshold with the right other parameters
  • Documentation improvements
    • Split Peak_detection page into smaller and more specific pages
  • Let the user choose how code is parallellized, as suggested by BiocParallel documentation.
  • Replace furr/future parallellization loops with BiocParallel. Provides a warning in case a future::plan() has been set.
  • Demote Imports to Suggests: SummarizedExpriment, S4Vectors, ggrepel, GGally
  • Remove dependencies: tidyselect, assertthat, plyr, furrr
  • Add download_MTBLS242() function to help download the data for the tutorial
  • Skip mixOmics test if affected by mixOmicsTeam/mixOmics#199
  • Fix auto setting of the baseline threshold for the peak detection

AlpsNMR 3.3.4 (2021-09-16)

  • Fix issue with PCA plots not working as expected
  • Ensure NMRExperiment names are not duplicated in a dataset (closes #44)
  • Fix issue with some title file formatting in Bruker samples (closes #46)
  • Export groups in to_ChemoSpec
  • License since AlpsNMR was released has alwayd been MIT as stated in the bioinformatics paper

AlpsNMR 3.1.5 (2021-3-31)

  • Removed warning about future_options deprecation

AlpsNMR 3.1.4 (2021-1-20)

  • bug fix loading bruker files

AlpsNMR 3.1.3 (2020-11-19)

  • Added instructions to follow a longer tutorial
  • nmr_pca_outliers_plot modified to show names in all boundaries of the plot

AlpsNMR 3.1.2 (2020-11-04)

  • Bug fix related with Bioconductor Renviron variable R_CHECK_LENGTH_1_CONDITION

AlpsNMR 3.1.1 (2020-10-30)

  • Modified order of author list

AlpsNMR 3.1.0 (2020-10-22)

  • Package accepted in bioconductor

AlpsNMR 2.99.93 (2020-10-22)

  • Héctor removed as maintainer to ensure a single point of contact

AlpsNMR 2.99.92 (2020-10-22)

  • Héctor added as maintainer

AlpsNMR 2.99.91 (2020-10-22)

  • test changed

AlpsNMR 2.99.9 (2020-10-22)

  • Added Héctor ass author
  • Bug fix in nmr_read_bruker_fid

AlpsNMR 2.99.8 (2020-10-22)

  • Deletion of tutorial and download_MTBLS242_demo.R

AlpsNMR 2.99.7 (2020-10-19)

  • Bugs in import/export functions to SummarizedExperiment solved

AlpsNMR 2.99.6 (2020-10-19)

  • Added import/export options form nmr_dataset_1D to SummarizedExperiment
  • Added import/export options form nmr_dataset_peak_table to SummarizedExperiment

AlpsNMR 2.99.5 (2020-10-14)

  • Bug in bp_kfold_VIP_analysis solved
  • Several packages moved from import to depends
  • Reexport of some functions removed
  • to_rDolphin_blood code reorganized
  • Typos removed from tutorial
  • norm_pqn_diagnostic$norm_factor used in tutorial instead of plot it
  • Parallel changed for BiocParallel

AlpsNMR 2.99.4 (2020-09-28)

  • Warning in plot_interactive function added
  • Suppressed other warnings of plot_interactive function

AlpsNMR 2.99.3 (2020-09-21)

  • sapply calls changed for vapply
  • Bioconductor installation instructions included
  • MIT license removed
  • LazyData: TRUE removed
  • Excessive print statements removed from vignettes
  • sessionInfo() added to end of vignettes
  • Created inst/script directoy to describe inst/extdata source and creation #TODO falta rellenar el archivo
  • Commented out code removed

AlpsNMR 2.99.2 (2020-08-26)

  • AlpsNMR.Rproj removed from git repository
  • Reduced demo dataset to avoid package size > 5 MB
  • Modified introduction to alpsnmr vignette and some tests to work with reduced demo dataset

AlpsNMR 2.99.1 (2020-08-25)

  • AlpsNMR.Rproj added to gitignore
  • Modified examples to avoid create files in main package folder

AlpsNMR 2.99.0 (2020-08-24)

  • Added bootstrap and permutation method and some plots related to it
  • Minor modifications for bioconductor submision

AlpsNMR 2.5.9002 (2020-05-25)

  • Changes to pass BiocCheck
  • Added permutation test and permutation test plot to nmr_data_analysis

AlpsNMR 2.4.9002 (2020-05-13)

  • Changes to pass checks for R4

AlpsNMR 2.3.3.9002

  • NIHS_specific removed
  • Tests coverage up to 30%
  • Update of save_profiling_plots
  • Add tutorial
  • Remotes installation
  • nmr_diagnose is deprecated. Since nmr_diagnose was only used for getting extra normalization information, it was been replaced with nmr_normalize_extra_info that offers a less confusing name.

AlpsNMR 2.3.3.9001

  • Add nmr_identify_regions_cell function
  • Add documentation of HMDB_cell
  • Vignettes updated
  • New functions to apply multilevel statistics
  • Update of README file

AlpsNMR 2.3.3

  • Change of nmr_identify_regions_blood function
  • Add nmr_identify_regions_urine function
  • Add documentation of HMDB_urine
  • Add computes_peak_width_ppmfunction for nmr_integrate_peak_positions
  • New get_integration_with_metadata
  • Vignettes updated
  • New functions to apply machine learning to proccessed datasets

AlpsNMR 2.3.2

  • Inclusion of baseline removal using assymetric least squares
  • Change the baselineThresh to NULL so it is autodetected
  • Vignettes updated including baseline removal
  • Bug correction in nmr_baseline_threshold
  • Elimination of package vignettes (there is an error to be solved there)
  • New nmr_identify_regions function
  • Add documentation of HMDB_blood
  • New files_to_rDolphin function

AlpsNMR 2.3.1.9000

  • Rename package from NIHSnmr to AlpsNMR

NIHSnmr 2.3.1

  • Change SNR.Th value from 3 to 4 in pipeline_example.R
  • Update installation instructions
  • Last version form Sergio (changes not significant since 2.3.0)

NIHSnmr 2.3.0

  • Improve installation instructions under R<3.5
  • nmr_peak_detection_tune_snr function added.
  • Minor bug fixes

NIHSnmr 2.2.0

  • Improve installation instructions
  • Clarify Add metadata vignette
  • Add normalization diagnostics
  • Add some data analysis helpers
  • Enable parallellization for sample loading, peak detection and data analysis helpers
  • Do not set negative area values to zero, to avoid biasing variances
  • Add metadata from a single tidy excel function
  • Add nmr_diagnose to get and set diagnostic information
  • Add nmr_diagnose support to nmr_normalize
  • Minor bug fixes

NIHSnmr 2.1.0

  • Documentation improvements
  • nmr_dataset_peak_table object for peak detection results

NIHSnmr 2.0.0

  • Too many changes to be listed here. Check the vignette for a summary of all the features. Use browseVignettes("NIHSnmr").

NIHSnmr 1.2.0

Breaking changes

  • Rename injection_id to NMRExperiment.

  • nmr_dataset_load and nmr_dataset_save now use readRDS and saveRDS instead of load and save. This is the right approach to serialize single R objects. If you need a script to convert previously saved datasets (created using nmr_dataset_save) please use NIHSnmr:::nmr_dataset_load_old_and_save("your_old_file.RData", "your_old_file.RDS") to convert the files. Sorry for the inconvenience, but the sooner we fix this the better.

  • filter to select a subset of samples from an nmr_dataset object has been adapted to dplyr >= 0.7.4. Unless you used the .dots argument in your calls there is no need to change anything. This means we now use a tidy evaluation syntax for filter.

  • nmr_get_metadata() returns always a data frame / tibble, even when only a single column is requested. It also always includes the "NMRExperiment" column.

  • nmr_dataset object has two tables metadata and metadata_ext. The metadata_ext table includes all the metadata we add with nmr_add_metadata while metadata has the internal metadata (acquisition parameters, etc). Please use nmr_get_metadata(nmr_dataset) instead of nmr_dataset$metadata.

Other changes

  • Remove workaround to dplyr issue: tidyverse/dplyr#2203 (Sergio Oller reported and fixed the issue, dplyr-0.7.0 is fixed)

  • The Bruker title file has quite a free format definition. A title file can contain lines like "Field value" or "Field value ;" or simply "value". The heuristics to parse the title file have been improved.

  • Depend on tidyr 0.8.1. tidyr 0.8.0 had a bug that we reported (and for which we also provided a fix): tidyverse/tidyr#419

  • nmr_get_metadata gives a warning if the user asks for metadata columns that are missing.

  • New nmr_integrate_regions function.

  • nmr_normalize accepts pqn normalization.