Base class for contrast analysis facades

Base class for contrast analysis facades

Base class for contrast analysis facades

Value

An R6 class generator.

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(): 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.

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(), 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

prolfqua::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

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

---

Method get_config()

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

Usage

ContrastsFacadeBase$get_config()

---

Method get_contrasts()

get contrast results, stamped with the facade key

Usage

ContrastsFacadeBase$get_contrasts(...)

Arguments

...

passed to the inner contrast object's get_contrasts

---

Method get_missing()

get subject x contrast pairs that could not be estimated

Usage

ContrastsFacadeBase$get_missing()

---

Method get_Plotter()

get ContrastsPlotter

Usage

ContrastsFacadeBase$get_Plotter(...)

Arguments

...

passed to the inner contrast object's get_Plotter

---

Method to_wide()

convert results to wide format

Usage

ContrastsFacadeBase$to_wide(...)

Arguments

...

passed to the inner contrast object's to_wide

---

Method 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