adjust_p_values         adjust columns
AggregateLimpa          AggregateLimpa
AggregateMedpolish      AggregateMedpolish
AggregateRlm            AggregateRlm
AggregateTopN           AggregateTopN
AnalysisConfiguration   Analysis Configuration
annotation_add_contrasts
                        DRY function: process and export annotated
                        contrasts
AnovaExtractor          R6 class for extracting ANOVA results as a data
                        frame
build_contrast_analysis
                        Build a contrast analysis using one of several
                        statistical methods
build_model             Build protein models from data
build_model_glm_peptide
                        Build Firth logistic model for nested LFQData
build_model_glm_protein
                        Build Firth logistic model for aggregated
                        LFQData
build_model_impute      Build protein models with LOD imputation for
                        failed fits
build_model_limma       Build limma model from LFQData
build_model_limma_impute
                        Build limma model with LOD imputation for
                        failed proteins
build_model_limma_voom
                        Build limma model with vooma precision weights
                        (proteomics)
build_model_limma_voom_impute
                        Build limma-voom model with LOD imputation for
                        failed proteins
build_model_limpa       Build limpa vooma model from aggregated LFQData
center_to_reference_cfg
                        center to reference
ContrastConfiguration   Contrast Configuration
Contrasts               Estimate contrasts using Wald Test
ContrastsBinomialNestedFacade
                        Quasibinomial detection-count facade for nested
                        input
ContrastsDEqMSFacade    DEqMS contrast analysis facade
ContrastsDEqMSVoomFacade
                        DEqMS contrast analysis with vooma weights
                        facade
ContrastsFirth          Estimate contrasts using Wald Test
ContrastsFirthFacade    Firth logistic missingness contrast analysis
                        facade
ContrastsFirthNestedFacade
                        Firth logistic missingness contrast analysis
                        facade for nested input
ContrastsInterface      Base class for all Contrasts classes
ContrastsLimma          Limma-based contrasts (direct limma pipeline)
ContrastsLimmaFacade    Limma contrast analysis facade
ContrastsLimmaImputeFacade
                        Limma contrast analysis with LOD imputation
                        facade
ContrastsLimmaVoomFacade
                        Limma-voom contrast analysis facade
ContrastsLimmaVoomImputeFacade
                        Limma-voom contrast analysis with LOD
                        imputation facade
ContrastsLimpaFacade    Limpa contrast analysis facade
ContrastsLimpaNestedFacade
                        Limpa contrast analysis facade for nested input
ContrastsLmerNestedFacade
                        Lmer (mixed-model) contrast analysis facade for
                        nested input
ContrastsLMFacade       LM contrast analysis facade
ContrastsLMImputeFacade
                        LM contrast analysis with LOD imputation facade
ContrastsModerated      Limma moderated contrasts
ContrastsModeratedDEqMS
                        DEqMS count-dependent moderated contrasts
ContrastsPlotter        plot contrasts
ContrastsRfitFacade     Rfit rank-based regression contrast analysis
                        facade
ContrastsRfitImputeFacade
                        Rfit rank-regression contrast analysis with LOD
                        imputation facade
ContrastsRLMFacade      RLM contrast analysis facade
ContrastsROPECA         ROPECA reproducibility-optimization method
ContrastsROPECANestedFacade
                        ROPECA contrast analysis facade for nested
                        input
ContrastsTable          holds results when contrasts are added.
df.residual.rfit_prolfqua
                        Residual degrees of freedom for an augmented
                        rfit fit
FACADE_REGISTRY         Registry of available contrast facade classes
find_package_file       find file stored in package
generate_contrasts      Combined generate_contrasts
generate_contrasts_for_factor
                        Single-factor contrasts (pairwise comparisons)
get_uniprot_id_from_fasta_header
                        Extracts uniprot ID
group_label             group label function
HierarchyCountsSample   Count distinct elements for each level of
                        hierarchy per sample
impute_from_model       Fill missing responses with predictions from
                        per-subject linear models
interaction_contrasts   Interaction contrasts (difference of
                        differences)
INTERNAL_FUNCTIONS_BY_FAMILY
                        Internal Functions by category
is_contaminant          Detect contaminant identifiers
is_decoy                Detect decoy / reverse-database identifiers
level_specific_contrasts
                        Level-specific contrasts (per secondary level)
LFQData                 LFQData R6 class
LFQDataPlotter          LFQDataPlotter -- Create various visualization
                        of the LFQdata
LFQDataStats            Decorates LFQData with methods to compute
                        statistics of interactions
LFQDataSummariser       Summarize LFQData
LFQDataToSummarizedExperiment
                        converts LFQData object to SummarizedExperiment
LFQDataTransformer      Decorate LFQData with Methods for transforming
                        Intensities
list_facades            List currently registered contrast facades
list_to_AnalysisConfiguration
                        read minimal yaml to reconstruct configuration
list_to_ContrastConfiguration
                        Rebuild a ContrastConfiguration from a list
lookup_facade           Look up a contrast facade by short name
LR_test                 Likelihood ratio test
main_effect_contrasts   main effects contrasts
matrix_to_tibble        matrix or data.frame to tibble (taken from
                        tidyquant)
merge_contrasts_results
                        Merge contrast results coming from two
                        different model.
MissingHelpers          Group statistics and limit of detection
Model                   R6 class representing modelling result
ModelFirth              R6 class representing modelling result
ModelInterface          R6 interface class representing modelling
                        result
ModelLimma              R6 class representing a limma modelling result
nr_children_experiment
                        Max nr_children across samples per hierarchy
                        unit
nr_features_experiment
                        Count distinct child features per hierarchy
                        unit
nr_obs_sample           Aggregates e.g. protein abundances from peptide
                        abundances
PACKAGE_DATA            Package Data
pivot_model_contrasts_to_wide
                        pivot model contrasts matrix to wide format
                        produced by 'contrasts_linfct' and ...
prolfqua_data           load data from prolfqua
R6_extract_values       Extract all value slots in an R6 object
register_facade         Register a contrast facade class
setup_analysis          Setup a tidy table compatible with a
                        'AnalysisConfiguration'
sigma.rfit_prolfqua     Scale estimate for an augmented rfit fit
sim_lfq_data            simulate protein level data with two groups
sim_lfq_data_2factor_config
                        Simulate data, protein, with config with 2
                        factors Treatment and Background
sim_lfq_data_peptide_config
                        Simulate data, protein and peptide, with config
sim_lfq_data_protein_config
                        Simulate data, protein, with config
strategy_binomial       Create a quasibinomial detection-count strategy
strategy_limma          Create limma modelling strategy
strategy_limpa          Create limpa modelling strategy
strategy_logistf        Create Firth's logistic regression strategy
StrategyBinomial        Quasibinomial detection-count strategy
StrategyLimma           R6 class for limma modelling strategy
StrategyLimpa           R6 class for limpa modelling strategy
StrategyLM              Linear model strategy (R6 class)
StrategyLmer            Linear mixed-effects model strategy (R6 class)
StrategyLogistf         Firth's logistic regression strategy (R6 class)
StrategyRfit            Rank-based regression strategy (R6 class)
StrategyRLM             Robust linear model strategy (R6 class)
summarize_stats_factors
                        compute var sd etc for all factor levels
table_facade            table facade to easily switch implementations
upset_interaction_missing_stats
                        UpSetR plot from interaction_missing_stats
vcov.rfit_prolfqua      Named variance-covariance matrix for an
                        augmented rfit fit
volcano_plotly          volcano plotly
which_missing           add missing values to x vector based on the
                        values of x
