NEWS

NADIA 0.99.2

Changes made in response to the Bioconductor review (#186).

NADIA no longer sets the random seed; call set.seed() to reproduce results. The seed arguments have been removed, and pattern_profiler_analysis() replaces seeds with n_starts.
61 helper functions used by the metric and benchmarking functions are no longer exported (reducing the number of exported functions from 111 to 50; 51 with the new preprocess_se()). The high-level functions continue to return all previously available outputs.
Protein score columns are PG.Score and PG.Score.RunWise_* in every format, instead of PG.Cscore; the original report metric is preserved in the nadia_labels attribute. Older tables and .nadia files can still be loaded.
imp_method = "missForest" now treats proteins as observations, as MsCoreUtils does; observations = "samples" retains the orientation used by NAguideR.
imp_method = "nbavg" has been removed, and bpca no longer accepts nPcs.

process_proteomics() accepts a SummarizedExperiment through the new import function preprocess_se().
export_format also applies to the exported matrices.

limma, rrcovNA, pROC and MsCoreUtils move to Imports; highcharter, reactable and paletteer move to Suggests; readr is removed. The availability of each suggested package is checked before use, and an installation command is provided if it is missing.
Imputation methods zero, min, with, MinDet, MinProb, QRILC, bpca and missForest, along with vsn normalization, now use MsCoreUtils and produce the same results as before.

Batch correction with protected covariates no longer discards measured values: proteins that cannot be corrected while protecting the covariates receive batch-only correction.
All plotting functions resolve palettes consistently; an unknown palette name raises an error.
Heatmaps accept partial row annotations, preserve condition colors in comparison-specific heatmaps and no longer modify ComplexHeatmap options.
Interactive tables on the same page no longer interfere with each other. Excel export preserves text that starts with digits, and condition names containing underscores are accepted.
Exported tables quote fields that contain tabs, newlines or quotes.
.nadia files restore the processing result exactly, except for the precision weights produced by limpa.
im_prepare_se() accepts norm_method = "log2".
A Parquet export without arrow fails before the analysis starts.

Initial Bioconductor submission.

Import of protein-level reports from Spectronaut (preprocess_spectronaut()), DIA-NN (preprocess_diann()) and Proteome Discoverer, including both TMT (preprocess_tmt()) and label-free (preprocess_lfq()).
process_proteomics() runs normalization (13 methods), optional batch correction, imputation (20 methods, including the two-stage MAR/MNAR combo strategy) and differential abundance analysis with limma or limpa.
Each protein's missingness is reported alongside its fold change: across the experiment, within the comparison and within each condition (MissGlobal, MissComp, MissCND1, MissCND2).
Evaluation of normalization and imputation methods (normalization_metrics(), imputation_metrics()) and spike-in benchmarking with OpDEA metrics (benchmarking_proteomics(), benchmarking_multiple()).
Soft clustering of abundance profiles with Mfuzz (pattern_profiler_analysis()).
Interactive and static figures (volcano plots, boxplots, PCA plots, heatmaps and cluster profiles) and interactive result tables.
write_nadia() and read_nadia() save and load a complete analysis in a single DuckDB file.
Example dataset nadia_dia and trimmed example reports in inst/extdata/.