NEWS.md
ggplot2::qplot()
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.
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.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.
names(dataset) <- c("Sample1", "Sample2").axis = NULL is given in nmr_interpolate_1D()
nmr_dataset object.future package (#65, thanks to @HenrikBengtsson)plot_interactive now accepts an overwrite argument to avoid asking the user interactivelynmr_detect_peaks_tune_snr to tune the SNR threshold with the right other parametersdownload_MTBLS242() function to help download the data for the tutorialnmr_data_analysis
save_profiling_plots
nmr_normalize_extra_info that offers a less confusing name.nmr_identify_regions_cell functionHMDB_cell
nmr_identify_regions_blood functionnmr_identify_regions_urine functionHMDB_urine
computes_peak_width_ppmfunction for nmr_integrate_peak_positions
get_integration_with_metadata
nmr_identify_regions functionHMDB_blood
files_to_rDolphin function