glyclean 0.15.0

Breaking changes

• Deprecated automatic-preprocessing arguments have been removed: qc_name from auto_clean(), auto_impute(), auto_normalize(), and auto_remove(); to_try from auto_impute() and auto_normalize(); and impute_to_try and normalize_to_try from auto_clean(). (#20)
• Normalization, imputation, filtering, CoDA, and batch-correction functions now require a glyexp::GlycomicSE, glyexp::GlycoproteomicSE, or legacy glyexp::experiment() object; matrix inputs error and should first be wrapped in a supported container. (#18, #19)

New features

• All preprocessing and QC functions now accept glyexp::GlycomicSE, glyexp::GlycoproteomicSE, legacy glyexp::experiment(), and plain SummarizedExperiment objects (for experiment type "others"), while preserving their class and metadata. (#19, #24)

Minor improvements and bug fixes

• aggregate() now processes large glycoproteomics experiments substantially faster while preserving group order and metadata. (#21)
• auto_clean() now removes glycoproteomics variables with excessive missingness before the first normalization step. (#23)