Base class for contrast analysis facades
Base class for contrast analysis facades
Details
Holds the fields and delegating methods shared by every facade in
ContrastsFacades.R and ContrastsChildToParentFacades.R.
Subclasses implement the unique pipeline wiring in initialize() (build
the model, build the inner contrast object, store self$.lfqdata /
self$.contrast_names) and set self$facade_name to their registry
key. The limma family additionally sets self$.drop_na_diff <- TRUE to
drop rows whose fold change could not be estimated.
get_contrasts() delegates to the inner contrast object and then stamps
the facade key into modelName via .stamp_facade_identity();
rescue/imputation state is carried in the estimate_type column set by
the inner contrast classes.
See also
Other modelling:
AnovaExtractor,
Contrasts,
ContrastsDEqMSFacade,
ContrastsDEqMSVoomFacade,
ContrastsFirth,
ContrastsFirthFacade,
ContrastsFirthNestedFacade,
ContrastsLMFacade,
ContrastsLMImputeFacade,
ContrastsLMMissingFacade,
ContrastsLimma,
ContrastsLimmaFacade,
ContrastsLimmaImputeFacade,
ContrastsLimmaVoomFacade,
ContrastsLimmaVoomImputeFacade,
ContrastsLimpaFacade,
ContrastsLimpaNestedFacade,
ContrastsLmerNestedFacade,
ContrastsMissing,
ContrastsModerated,
ContrastsModeratedDEqMS,
ContrastsPlotter,
ContrastsRLMFacade,
ContrastsROPECA,
ContrastsROPECANestedFacade,
ContrastsRfitFacade,
ContrastsRfitImputeFacade,
ContrastsTable,
INTERNAL_FUNCTIONS_BY_FAMILY,
LR_test(),
Model,
ModelFirth,
ModelLimma,
StrategyLM,
StrategyLimma,
StrategyLimpa,
StrategyLmer,
StrategyLogistf,
StrategyRLM,
StrategyRfit,
build_contrast_analysis(),
build_model(),
build_model_glm_peptide(),
build_model_glm_protein(),
build_model_impute(),
build_model_limma(),
build_model_limma_impute(),
build_model_limma_voom(),
build_model_limma_voom_impute(),
build_model_limpa(),
build_model_logistf(),
compute_borrowed_variance(),
compute_borrowed_variance_limma(),
compute_contrast(),
compute_lmer_contrast(),
contrasts_fisher_exact(),
df.residual.rfit_prolfqua(),
get_anova_df(),
get_complete_model_fit(),
get_p_values_pbeta(),
group_label(),
impute_refit_singular(),
is_singular_lm(),
linfct_all_possible_contrasts(),
linfct_factors_contrasts(),
linfct_from_model(),
linfct_matrix_contrasts(),
list_facades(),
lookup_facade(),
merge_contrasts_results(),
model_analyse(),
model_summary(),
moderated_p_deqms(),
moderated_p_deqms_long(),
moderated_p_limma(),
moderated_p_limma_long(),
new_imputed_model(),
pivot_model_contrasts_to_wide(),
plot_lmer_peptide_predictions(),
register_facade(),
sigma.rfit_prolfqua(),
sim_build_models_lm(),
sim_build_models_lmer(),
sim_build_models_logistf(),
sim_make_model_lm(),
sim_make_model_lmer(),
strategy_limma(),
strategy_limpa(),
strategy_logistf(),
summary_ROPECA_median_p.scaled(),
unregister_facade(),
vcov.rfit_prolfqua()
Super class
prolfqua::ContrastsInterface -> ContrastsFacadeBase
Public fields
modelfitted model object
contrastinner contrast object the facade delegates to
.lfqdatastored reference to the input LFQData (used by get_missing)
.contrast_namesnames of the requested contrasts
facade_nameregistry key stamped into the modelName column
.drop_na_diffdrop rows with NA diff (limma family); default FALSE
Methods
Inherited methods
prolfqua::ContrastsInterface$column_description()prolfqua::ContrastsInterface$contrast_summary_table()prolfqua::ContrastsInterface$extra_artifacts()prolfqua::ContrastsInterface$filter_significant()prolfqua::ContrastsInterface$get_config()prolfqua::ContrastsInterface$get_contrast_sides()prolfqua::ContrastsInterface$get_ora()prolfqua::ContrastsInterface$get_rank()
Method get_Plotter()
get ContrastsPlotter