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Register a contrast facade class

Source: R/ContrastsFacades.R
register_facade.Rd

Adds an entry to the prolfqua facade registry so that lookup_facade (and downstream consumers such as prolfquapp::R6_DEAnalyse$build_facade()) can resolve it by short name. Intended for downstream packages that ship additional modelling backends (e.g. prolfquasaint) and want to plug into the same dispatch path as the built-in facades.

Usage

register_facade(
  name,
  class,
  needs,
  package = "prolfqua",
  needs_saint_annotation = FALSE,
  ...
)

Arguments

name

short method name, e.g. "saint".

class

character; R6 facade class name to instantiate.

needs

one of "same" (facade emits contrasts at the same hierarchy level as its input e.g. protein -> protein FC, peptide -> peptide FC) or "nested" (facade takes child-level input and emits parent-level contrasts, e.g. peptide -> protein FC).

package

package the facade class lives in. Defaults to "prolfqua".

needs_saint_annotation

TRUE if the backend requires annotation reading in SAINT mode (bait / control columns). Default FALSE.

...

additional fields stored on the registry entry, available to consumers via lookup_facade.

Value

The registered entry (invisibly).

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, ContrastsTable, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, ModelFirth, ModelLimma, StrategyLM, StrategyLimma, StrategyLimpa, StrategyLmer, StrategyLogistf, StrategyRLM, 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(), 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_lm_imputed(), pivot_model_contrasts_to_wide(), plot_lmer_peptide_predictions(), 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()

Examples

lookup_facade("lm")$class
#> [1] "ContrastsLMFacade"
# downstream packages call this from .onLoad():
# prolfqua::register_facade("saint", class = "ContrastsSAINTFacade",
#                           needs = "same", package = "prolfquasaint",
#                           needs_saint_annotation = TRUE)