Base class for contrast analysis facades

Holds the fields and delegating methods shared by every facade in ContrastsFacades.R and ContrastsChildToParentFacades.R. Subclasses implement the unique pipeline wiring in initialize(): they call the private .setup() (input-shape check, self$.lfqdata, self$.contrast_names, self$facade_name), then build the model and the inner contrast object. get_config() defaults to the inner contrast object's configuration. The limma family additionally sets self$.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.

Value

An R6 class generator.

See also

Other modelling: AnovaExtractor, Contrasts, ContrastsDEqMSFacade, ContrastsDEqMSVoomFacade, ContrastsFirth, ContrastsFirthFacade, ContrastsFirthNestedFacade, ContrastsHurdleFacade, ContrastsHurdleNestedFacade, ContrastsLMFacade, ContrastsLMImputeFacade, ContrastsLimma, ContrastsLimmaFacade, ContrastsLimmaImputeFacade, ContrastsLimmaVoomFacade, ContrastsLimmaVoomImputeFacade, ContrastsLimpaFacade, ContrastsLimpaNestedFacade, ContrastsLmerNestedFacade, 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(), df.residual.rfit_prolfqua(), get_anova_df(), get_complete_model_fit(), get_p_values_pbeta(), group_label(), impute_from_model(), impute_refit_singular(), 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(), new_imputed_model(), pivot_model_contrasts_to_wide(), 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(), vcov.rfit_prolfqua()

Super class

ContrastsInterface -> ContrastsFacadeBase

Public fields

model

fitted model object

contrast

inner contrast object the facade delegates to

.lfqdata

stored reference to the input LFQData (used by get_missing)

.contrast_names

names of the requested contrasts

facade_name

registry key stamped into the modelName column

.drop_na_diff

drop rows with NA diff (limma family); default FALSE

Methods

Public methods

• ContrastsFacadeBase$get_config()

• ContrastsFacadeBase$get_contrasts()

• ContrastsFacadeBase$get_missing()

• ContrastsFacadeBase$get_Plotter()

• ContrastsFacadeBase$to_wide()

• ContrastsFacadeBase$clone()

Inherited methods

• ContrastsInterface$column_description()
• ContrastsInterface$contrast_summary_table()
• ContrastsInterface$extra_artifacts()
• ContrastsInterface$filter_significant()
• ContrastsInterface$get_contrast_sides()
• ContrastsInterface$get_ora()
• ContrastsInterface$get_rank()

---

ContrastsFacadeBase$get_config()

get the ContrastConfiguration; defaults to the inner contrast object's configuration

Usage

ContrastsFacadeBase$get_config()

---

ContrastsFacadeBase$get_contrasts()

get contrast results, stamped with the facade key

Usage

ContrastsFacadeBase$get_contrasts(...)

Arguments

...

passed to the inner contrast object's get_contrasts

---

ContrastsFacadeBase$get_missing()

get subject x contrast pairs that could not be estimated

Usage

ContrastsFacadeBase$get_missing()

---

ContrastsFacadeBase$get_Plotter()

get ContrastsPlotter

Usage

ContrastsFacadeBase$get_Plotter(...)

Arguments

...

passed to the inner contrast object's get_Plotter

---

ContrastsFacadeBase$to_wide()

convert results to wide format

Usage

ContrastsFacadeBase$to_wide(...)

Arguments

...

passed to the inner contrast object's to_wide

---

ContrastsFacadeBase$clone()

The objects of this class are cloneable with this method.

Usage

ContrastsFacadeBase$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

facade <- ContrastsFacadeBase$new()
inherits(facade, "ContrastsFacadeBase")
#> [1] TRUE